4tnk - Revision history

OCA at 07:20, 27 September 2023

2023-09-27T07:20:02Z

←Older revision		Revision as of 07:20, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tnk]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TNK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tnk]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TNK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 5.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [https://pdbe.org/4tnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [https://www.ebi.ac.uk/pdbsum/4tnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnk ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [https://pdbe.org/4tnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [https://www.ebi.ac.uk/pdbsum/4tnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnk ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	==See Also==		==See Also==
	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]		*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
-	*[[Photosystem II\|Photosystem II]]	+	*[[Photosystem II 3D structures\|Photosystem II 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:46, 15 March 2023

2023-03-15T10:46:58Z

←Older revision		Revision as of 10:46, 15 March 2023
Line 3:		Line 3:
	<StructureSection load='4tnk' size='340' side='right'caption='[[4tnk]], [[Resolution\|resolution]] 5.20Å' scene=''>		<StructureSection load='4tnk' size='340' side='right'caption='[[4tnk]], [[Resolution\|resolution]] 5.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4tnk]] is a 40 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thermosynechococcus_elongatus~~ Thermosynechococcus ~~elongatus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4TNK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4tnk]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TNK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [https://pdbe.org/4tnk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [https://www.ebi.ac.uk/pdbsum/4tnk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnk ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [~~http~~://pdbe.org/4tnk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4tnk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~PSBL_THEEB PSBL_THEEB~~]~~] Required for PSII activity (By similarity). [[http://www.uniprot.org/uniprot/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem~~ II (PSII)~~.[HAMAP~~-~~Rule~~:MF_01329] [[http://www.uniprot.org/uniprot/PSBA1_THEEB PSBA1_THEEB]] This is one of the two reaction center proteins of photosystem II. [[http://www.uniprot.org/uniprot/PSBX_THEEB PSBX_THEEB]] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.<ref>PMID:11230572</ref> [[http://www.uniprot.org/uniprot/CY550_THEEB CY550_THEEB]] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. It is not essential for growth under normal conditions but is required under low CO(2) ~~concentrations~~.~~[HAMAP-Rule:MF_01378] [[http://www.uniprot.org/uniprot/PSBO_THEEB PSBO_THEEB]] MSP binds to~~ a ~~putative Mn-binding protein~~ and ~~keeps 2 of the 4 Mn-atoms associated with PSII (By similarity)~~. ~~[[http:~~//~~www.uniprot.org/uniprot/PSBF_THEEB PSBF_THEEB]] This b-type cytochrome is tightly associated with the~~ reaction center of ~~photosystem II and possibly is part of the water-oxidation complex (By similarity)~~.[HAMAP-Rule:~~MF_00643~~] ~~[[http~~://www.uniprot.org/uniprot/PSBJ_THEEB PSBJ_THEEB]] This protein is a component of the reaction center of photosystem II (By similarity). [[http://www.uniprot.org/uniprot/PSBZ_THEEB PSBZ_THEEB]] Controls the interaction of photosystem II (PSII) cores with the light-harvesting antenna. May also aid in binding of PsbK, Ycf12 and the oxygen-evolving complex to PSII, at least in vitro.<ref>PMID:~~17967798~~</ref> ~~[[http://www.uniprot.org/uniprot/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.~~<ref>PMID:~~15653799~~</ref> [[http://www.uniprot.org/uniprot/PSBU_THEEB PSBU_THEEB]] Stabilizes the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protects the OEC against heat-induced inactivation (By similarity).[HAMAP-Rule:MF_00589] [[http://www.uniprot.org/uniprot/PSBI_THEEB PSBI_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [[http://www.uniprot.org/uniprot/PSBK_THEEB PSBK_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [[http://www.uniprot.org/uniprot/PSBE_THEEB PSBE_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex.[HAMAP-Rule:MF_00642]	+	[https://www.uniprot.org/uniprot/PSBA1_THEVB PSBA1_THEVB] Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbA) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.[HAMAP-Rule:MF_01379]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 30:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Photosystem II]]~~	+	[[Category: Thermosynechococcus vestitus BP-1]]
-	[[Category: Thermosynechococcus ~~elongatus~~]]	+	[[Category: Adams PD]]
-	[[Category: Adams~~, P D~~]]	+	[[Category: Alonso-Mori R]]
-	[[Category: Alonso-Mori, R]]	+	[[Category: Bergmann U]]
-	[[Category: Bergmann, U]]	+	[[Category: Bogan MJ]]
-	[[Category: Bogan~~, M J~~]]	+	[[Category: Boutet S]]
-	[[Category: Boutet, S]]	+	[[Category: Brewster A]]
-	[[Category: Brewster, A]]	+	[[Category: Chatterjee R]]
-	[[Category: Chatterjee, R]]	+	[[Category: DiFiore D]]
-	[[Category: DiFiore, D]]	+	[[Category: Echols N]]
-	[[Category: Echols, N]]	+	[[Category: Fry AR]]
-	[[Category: Fry~~, A R~~]]	+	[[Category: Gallo E]]
-	[[Category: Gallo, E]]	+	[[Category: Gildea RJ]]
-	[[Category: Gildea~~, R J~~]]	+	[[Category: Glatzel P]]
-	[[Category: Glatzel, P]]	+	[[Category: Gloeckner C]]
-	[[Category: Gloeckner, C]]	+	[[Category: Gul S]]
-	[[Category: Gul, S]]	+	[[Category: Han G]]
-	[[Category: Han, G]]	+	[[Category: Hattne J]]
-	[[Category: Hattne, J]]	+	[[Category: Hellmich J]]
-	[[Category: Hellmich, J]]	+	[[Category: Ibrahim M]]
-	[[Category: Ibrahim, M]]	+	[[Category: Kern J]]
-	[[Category: Kern, J]]	+	[[Category: Koglin JE]]
-	[[Category: Koglin~~, J E~~]]	+	[[Category: Koroidov S]]
-	[[Category: Koroidov, S]]	+	[[Category: Laksmono H]]
-	[[Category: Laksmono, H]]	+	[[Category: Lampe A]]
-	[[Category: Lampe, A]]	+	[[Category: Lassalle-Kaiser B]]
-	[[Category: Lassalle-Kaiser, B]]	+	[[Category: Messerschmidt M]]
-	[[Category: Messerschmidt, M]]	+	[[Category: Messinger J]]
-	[[Category: Messinger, J]]	+	[[Category: Milathianaki D]]
-	[[Category: Milathianaki, D]]	+	[[Category: Sauter NK]]
-	[[Category: Sauter~~, N K~~]]	+	[[Category: Seibert MM]]
-	[[Category: Seibert~~, M M~~]]	+	[[Category: Sierra RG]]
-	[[Category: Sierra~~, R G~~]]	+	[[Category: Skinner DE]]
-	[[Category: Skinner~~, D E~~]]	+	[[Category: Sokaras D]]
-	[[Category: Sokaras, D]]	+	[[Category: Stan CA]]
-	[[Category: Stan~~, C A~~]]	+	[[Category: Tran R]]
-	[[Category: Tran, R]]	+	[[Category: Uhlig J]]
-	[[Category: Uhlig, J]]	+	[[Category: Weng T-C]]
-	[[Category: Weng, T C]]	+	[[Category: Williams GJ]]
-	[[Category: Williams~~, G J~~]]	+	[[Category: Yachandra VK]]
-	[[Category: Yachandra~~, V K~~]]	+	[[Category: Yano J]]
-	[[Category: Yano, J]]	+	[[Category: Zouni A]]
-	[[Category: Zouni, A]]	+	[[Category: Zwart PH]]
-	[[Category: Zwart~~, P H]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Photosynthesis]]~~	+
-	~~[[Category: Water oxidation]]~~	+
-	~~[[Category: X-ray free electron laser~~]]	+

OCA at 08:36, 4 December 2019

2019-12-04T08:36:59Z

←Older revision		Revision as of 08:36, 4 December 2019
Line 1:		Line 1:

	==RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution==		==RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution==
-	<StructureSection load='4tnk' size='340' side='right' caption='[[4tnk]], [[Resolution\|resolution]] 5.20Å' scene=''>	+	<StructureSection load='4tnk' size='340' side='right'caption='[[4tnk]], [[Resolution\|resolution]] 5.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tnk]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tnk]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNK FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 4tnk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4tnk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
		+	*[[Photosystem II\|Photosystem II]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Photosystem II]]		[[Category: Photosystem II]]
	[[Category: Thermosynechococcus elongatus]]		[[Category: Thermosynechococcus elongatus]]

OCA at 12:04, 6 November 2017

2017-11-06T12:04:25Z

←Older revision		Revision as of 12:04, 6 November 2017
Line 1:		Line 1:
		+
	==RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution==		==RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution==
	<StructureSection load='4tnk' size='340' side='right' caption='[[4tnk]], [[Resolution\|resolution]] 5.20Å' scene=''>		<StructureSection load='4tnk' size='340' side='right' caption='[[4tnk]], [[Resolution\|resolution]] 5.20Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://pdbe.org/4tnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://pdbe.org/4tnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tnk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 4tnk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4tnk" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Photosystem II\|Photosystem II]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:44, 7 October 2015

2015-10-07T07:44:26Z

←Older revision		Revision as of 07:44, 7 October 2015
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://pdbe.org/4tnk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/PSBF_THEEB PSBF_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex (By similarity).[HAMAP-Rule:MF_00643] [[http://www.uniprot.org/uniprot/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[http://www.uniprot.org/uniprot/~~PSBJ_THEEB PSBJ_THEEB~~]] ~~This protein is a component of the reaction center~~ of photosystem II (~~By similarity~~). [[http://www.uniprot.org/uniprot/~~YCF12_THEEB YCF12_THEEB~~]] ~~A core subunit~~ of photosystem II ~~(PSII)~~.~~[HAMAP-Rule:MF_01329]~~ [[http://www.uniprot.org/uniprot/~~PSBZ_THEEB PSBZ_THEEB~~]] ~~Controls~~ the ~~interaction~~ of ~~photosystem II~~ (~~PSII~~) ~~cores with the light-harvesting antenna. May also aid in binding~~ of ~~PsbK, Ycf12 and the oxygen-evolving complex to PSII, at least in vitro~~.<ref>PMID:~~17967798~~</ref> [[http://www.uniprot.org/uniprot/~~PSBU_THEEB PSBU_THEEB~~]] ~~Stabilizes~~ the ~~structure of photosystem II~~ oxygen-evolving complex ~~(OEC), the ion environment~~ of ~~oxygen evolution and protects the OEC against heat-induced inactivation~~ (~~By similarity~~).[HAMAP-Rule:~~MF_00589~~] [[http://www.uniprot.org/uniprot/~~PSBT_THEEB PSBT_THEEB~~]] ~~Seems~~ to ~~play~~ a ~~role in the dimerization~~ of PSII.~~<ref>PMID:15653799</ref>~~ [[http://www.uniprot.org/uniprot/~~PSBI_THEEB PSBI_THEEB~~]] This ~~protein~~ is ~~a component of~~ the reaction center of photosystem II.[HAMAP-Rule:~~MF_01316~~] [[http://www.uniprot.org/uniprot/~~PSBA1_THEEB PSBA1_THEEB~~]] This is ~~one~~ of the ~~two~~ reaction center ~~proteins~~ of photosystem II. [[http://www.uniprot.org/uniprot/~~PSBX_THEEB PSBX_THEEB~~]] ~~Involved in~~ the ~~binding and/or turnover~~ of ~~quinones at the Q~~(B) ~~site~~ of ~~Photosystem II~~.<ref>PMID:~~11230572~~</ref> [[http://www.uniprot.org/uniprot/~~PSBK_THEEB PSBK_THEEB~~]] ~~This protein is~~ a ~~component~~ of the ~~reaction center~~ of photosystem II.[HAMAP-Rule:~~MF_00441~~] [[http://www.uniprot.org/uniprot/~~PSBO_THEEB PSBO_THEEB~~]] ~~MSP binds to a putative Mn-binding~~ protein ~~and keeps 2~~ of the ~~4 Mn-atoms associated with PSII (By similarity)~~. [[http://www.uniprot.org/uniprot/~~CY550_THEEB CY550_THEEB~~]] ~~Low-potential cytochrome c that plays~~ a ~~role in~~ the ~~oxygen-evolving complex~~ of photosystem II~~. It is not essential for growth under normal conditions but is required under low CO(2) concentrations~~.[HAMAP-Rule:~~MF_01378~~] [[http://www.uniprot.org/uniprot/PSBE_THEEB PSBE_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex.[HAMAP-Rule:MF_00642]	+	[[http://www.uniprot.org/uniprot/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[http://www.uniprot.org/uniprot/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[http://www.uniprot.org/uniprot/PSBA1_THEEB PSBA1_THEEB]] This is one of the two reaction center proteins of photosystem II. [[http://www.uniprot.org/uniprot/PSBX_THEEB PSBX_THEEB]] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.<ref>PMID:11230572</ref> [[http://www.uniprot.org/uniprot/CY550_THEEB CY550_THEEB]] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. It is not essential for growth under normal conditions but is required under low CO(2) concentrations.[HAMAP-Rule:MF_01378] [[http://www.uniprot.org/uniprot/PSBO_THEEB PSBO_THEEB]] MSP binds to a putative Mn-binding protein and keeps 2 of the 4 Mn-atoms associated with PSII (By similarity). [[http://www.uniprot.org/uniprot/PSBF_THEEB PSBF_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex (By similarity).[HAMAP-Rule:MF_00643] [[http://www.uniprot.org/uniprot/PSBJ_THEEB PSBJ_THEEB]] This protein is a component of the reaction center of photosystem II (By similarity). [[http://www.uniprot.org/uniprot/PSBZ_THEEB PSBZ_THEEB]] Controls the interaction of photosystem II (PSII) cores with the light-harvesting antenna. May also aid in binding of PsbK, Ycf12 and the oxygen-evolving complex to PSII, at least in vitro.<ref>PMID:17967798</ref> [[http://www.uniprot.org/uniprot/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.<ref>PMID:15653799</ref> [[http://www.uniprot.org/uniprot/PSBU_THEEB PSBU_THEEB]] Stabilizes the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protects the OEC against heat-induced inactivation (By similarity).[HAMAP-Rule:MF_00589] [[http://www.uniprot.org/uniprot/PSBI_THEEB PSBI_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [[http://www.uniprot.org/uniprot/PSBK_THEEB PSBK_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [[http://www.uniprot.org/uniprot/PSBE_THEEB PSBE_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex.[HAMAP-Rule:MF_00642]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4tnk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Photosystem II\|Photosystem II]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:01, 25 December 2014

2014-12-25T10:01:54Z

←Older revision		Revision as of 10:01, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4tnk]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4tnk]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PSBF_THEEB PSBF_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex (By similarity).[HAMAP-Rule:MF_00643] [[http://www.uniprot.org/uniprot/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[http://www.uniprot.org/uniprot/PSBJ_THEEB PSBJ_THEEB]] This protein is a component of the reaction center of photosystem II (By similarity). [[http://www.uniprot.org/uniprot/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[http://www.uniprot.org/uniprot/PSBZ_THEEB PSBZ_THEEB]] Controls the interaction of photosystem II (PSII) cores with the light-harvesting antenna. May also aid in binding of PsbK, Ycf12 and the oxygen-evolving complex to PSII, at least in vitro.<ref>PMID:17967798</ref> [[http://www.uniprot.org/uniprot/PSBU_THEEB PSBU_THEEB]] Stabilizes the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protects the OEC against heat-induced inactivation (By similarity).[HAMAP-Rule:MF_00589] [[http://www.uniprot.org/uniprot/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.<ref>PMID:15653799</ref> [[http://www.uniprot.org/uniprot/PSBI_THEEB PSBI_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [[http://www.uniprot.org/uniprot/PSBA1_THEEB PSBA1_THEEB]] This is one of the two reaction center proteins of photosystem II. [[http://www.uniprot.org/uniprot/PSBX_THEEB PSBX_THEEB]] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.<ref>PMID:11230572</ref> [[http://www.uniprot.org/uniprot/PSBK_THEEB PSBK_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [[http://www.uniprot.org/uniprot/PSBO_THEEB PSBO_THEEB]] MSP binds to a putative Mn-binding protein and keeps 2 of the 4 Mn-atoms associated with PSII (By similarity). [[http://www.uniprot.org/uniprot/CY550_THEEB CY550_THEEB]] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. It is not essential for growth under normal conditions but is required under low CO(2) concentrations.[HAMAP-Rule:MF_01378] [[http://www.uniprot.org/uniprot/PSBE_THEEB PSBE_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex.[HAMAP-Rule:MF_00642]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 25:
	[[Category: Photosystem II]]		[[Category: Photosystem II]]
	[[Category: Thermosynechococcus elongatus]]		[[Category: Thermosynechococcus elongatus]]
-	[[Category: Adams, P D.]]	+	[[Category: Adams, P D]]
-	[[Category: Alonso-Mori, R.]]	+	[[Category: Alonso-Mori, R]]
-	[[Category: Bergmann, U.]]	+	[[Category: Bergmann, U]]
-	[[Category: Bogan, M J.]]	+	[[Category: Bogan, M J]]
-	[[Category: Boutet, S.]]	+	[[Category: Boutet, S]]
-	[[Category: Brewster, A.]]	+	[[Category: Brewster, A]]
-	[[Category: Chatterjee, R.]]	+	[[Category: Chatterjee, R]]
-	[[Category: DiFiore, D.]]	+	[[Category: DiFiore, D]]
-	[[Category: Echols, N.]]	+	[[Category: Echols, N]]
-	[[Category: Fry, A R.]]	+	[[Category: Fry, A R]]
-	[[Category: Gallo, E.]]	+	[[Category: Gallo, E]]
-	[[Category: Gildea, R J.]]	+	[[Category: Gildea, R J]]
-	[[Category: Glatzel, P.]]	+	[[Category: Glatzel, P]]
-	[[Category: Gloeckner, C.]]	+	[[Category: Gloeckner, C]]
-	[[Category: Gul, S.]]	+	[[Category: Gul, S]]
-	[[Category: Han, G.]]	+	[[Category: Han, G]]
-	[[Category: Hattne, J.]]	+	[[Category: Hattne, J]]
-	[[Category: Hellmich, J.]]	+	[[Category: Hellmich, J]]
-	[[Category: Ibrahim, M.]]	+	[[Category: Ibrahim, M]]
-	[[Category: Kern, J.]]	+	[[Category: Kern, J]]
-	[[Category: Koglin, J E.]]	+	[[Category: Koglin, J E]]
-	[[Category: Koroidov, S.]]	+	[[Category: Koroidov, S]]
-	[[Category: Laksmono, H.]]	+	[[Category: Laksmono, H]]
-	[[Category: Lampe, A.]]	+	[[Category: Lampe, A]]
-	[[Category: Lassalle-Kaiser, B.]]	+	[[Category: Lassalle-Kaiser, B]]
-	[[Category: Messerschmidt, M.]]	+	[[Category: Messerschmidt, M]]
-	[[Category: Messinger, J.]]	+	[[Category: Messinger, J]]
-	[[Category: Milathianaki, D.]]	+	[[Category: Milathianaki, D]]
-	[[Category: Sauter, N K.]]	+	[[Category: Sauter, N K]]
-	[[Category: Seibert, M M.]]	+	[[Category: Seibert, M M]]
-	[[Category: Sierra, R G.]]	+	[[Category: Sierra, R G]]
-	[[Category: Skinner, D E.]]	+	[[Category: Skinner, D E]]
-	[[Category: Sokaras, D.]]	+	[[Category: Sokaras, D]]
-	[[Category: Stan, C A.]]	+	[[Category: Stan, C A]]
-	[[Category: Tran, R.]]	+	[[Category: Tran, R]]
-	[[Category: Uhlig, J.]]	+	[[Category: Uhlig, J]]
-	[[Category: Weng, T C.]]	+	[[Category: Weng, T C]]
-	[[Category: Williams, G J.]]	+	[[Category: Williams, G J]]
-	[[Category: Yachandra, V K.]]	+	[[Category: Yachandra, V K]]
-	[[Category: Yano, J.]]	+	[[Category: Yano, J]]
-	[[Category: Zouni, A.]]	+	[[Category: Zouni, A]]
-	[[Category: Zwart, P H.]]	+	[[Category: Zwart, P H]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Membrane protein]]		[[Category: Membrane protein]]

OCA at 06:45, 23 July 2014

2014-07-23T06:45:51Z

←Older revision		Revision as of 06:45, 23 July 2014
Line 11:		Line 11:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~phenix.refine~~ is a ~~program~~ within the ~~PHENIX package that supports crystallographic structure refinement against experimental~~ data ~~with a wide range~~ of ~~upper resolution limits using a large repertoire of model parameterizations. It has several automation features~~ and ~~is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user~~-~~defined refinement strategies can be applied to specific parts~~ of the ~~model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects.~~ X-ray ~~or neutron diffraction data can be used separately or jointly in refinement~~. ~~phenix.refine is tightly integrated into~~ the ~~PHENIX suite~~, ~~where it serves as a critical component in automated model building~~, ~~final structure refinement, structure validation and deposition to~~ the ~~wwPDB~~. ~~This paper presents~~ an ~~overview~~ of the ~~major phenix.refine features, with extensive literature references for readers interested~~ in ~~more detailed discussions~~ of the ~~methods~~.	+	The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 mus after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 mus after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 A. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.

-	~~Towards automated crystallographic structure refinement with phenix.refine~~.,~~Afonine PV~~, ~~Grosse~~-~~Kunstleve RW~~, Echols N, ~~Headd JJ~~, ~~Moriarty NW, Mustyakimov~~ M, ~~Terwilliger TC~~, ~~Urzhumtsev~~ A, Zwart PH, Adams PD ~~Acta Crystallogr D Biol Crystallogr~~. ~~2012 Apr~~;~~68(Pt 4)~~:~~352-67~~. doi:, 10.~~1107~~/~~S0907444912001308. Epub 2012 Mar 16~~. PMID:~~22505256~~<ref>PMID:~~22505256~~</ref>	+	Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.,Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glockner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK Nat Commun. 2014 Jul 9;5:4371. doi: 10.1038/ncomms5371. PMID:25006873<ref>PMID:25006873</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 07:25, 9 July 2014

2014-07-09T07:25:04Z

←Older revision		Revision as of 07:25, 9 July 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution==
		+	<StructureSection load='4tnk' size='340' side='right' caption='[[4tnk]], [[Resolution\|resolution]] 5.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4tnk]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TNK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TNK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4tnh\|4tnh]], [[4tni\|4tni]], [[4tnj\|4tnj]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4tnk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tnk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4tnk RCSB], [http://www.ebi.ac.uk/pdbsum/4tnk PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

-	~~The entry 4tnk is ON HOLD~~	+	Towards automated crystallographic structure refinement with phenix.refine.,Afonine PV, Grosse-Kunstleve RW, Echols N, Headd JJ, Moriarty NW, Mustyakimov M, Terwilliger TC, Urzhumtsev A, Zwart PH, Adams PD Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):352-67. doi:, 10.1107/S0907444912001308. Epub 2012 Mar 16. PMID:22505256<ref>PMID:22505256</ref>

-	~~Authors: Kern~~, J.~~, Tran, R~~., Alonso-Mori, R., ~~Koroidov~~, S., ~~Echols, N~~., ~~Hattne, J~~., ~~Ibrahim, M~~., ~~Gul, S~~., ~~Laksmono, H~~., ~~Sierra,~~ R.G., Gildea, R.J., Han, G., Hellmich, J., ~~Lassalle-Kaiser, B~~., ~~Chatterjee, R~~., ~~Brewster, A~~., ~~Stan, C.A~~., ~~Gloeckner, C~~., Lampe, A., ~~DiFiore~~, D., Milathianaki, D., ~~Fry, A~~.~~R.,~~ Seibert, M.M., ~~Koglin, J.E~~., ~~Gallo,~~ E.~~, Uhlig, J.,~~ Sokaras, D., ~~Weng, T.-~~C., ~~Zwart, P.H~~., ~~Skinner, D.E., Bogan, M.~~J., ~~Messerschmidt, M~~.~~, Glatzel, P.,~~ Williams, G.J., ~~Boutet, S~~., ~~Adams, P.D~~., Zouni, A., ~~Messinger, J., Sauter, N.K., Bergmann, U., Yano, J., Yachandra, V.K~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Photosystem II]]
		+	[[Category: Thermosynechococcus elongatus]]
		+	[[Category: Adams, P D.]]
		+	[[Category: Alonso-Mori, R.]]
		+	[[Category: Bergmann, U.]]
		+	[[Category: Bogan, M J.]]
		+	[[Category: Boutet, S.]]
		+	[[Category: Brewster, A.]]
		+	[[Category: Chatterjee, R.]]
		+	[[Category: DiFiore, D.]]
		+	[[Category: Echols, N.]]
		+	[[Category: Fry, A R.]]
		+	[[Category: Gallo, E.]]
		+	[[Category: Gildea, R J.]]
		+	[[Category: Glatzel, P.]]
		+	[[Category: Gloeckner, C.]]
		+	[[Category: Gul, S.]]
		+	[[Category: Han, G.]]
		+	[[Category: Hattne, J.]]
		+	[[Category: Hellmich, J.]]
		+	[[Category: Ibrahim, M.]]
		+	[[Category: Kern, J.]]
		+	[[Category: Koglin, J E.]]
		+	[[Category: Koroidov, S.]]
		+	[[Category: Laksmono, H.]]
		+	[[Category: Lampe, A.]]
		+	[[Category: Lassalle-Kaiser, B.]]
		+	[[Category: Messerschmidt, M.]]
		+	[[Category: Messinger, J.]]
		+	[[Category: Milathianaki, D.]]
		+	[[Category: Sauter, N K.]]
		+	[[Category: Seibert, M M.]]
		+	[[Category: Sierra, R G.]]
		+	[[Category: Skinner, D E.]]
		+	[[Category: Sokaras, D.]]
		+	[[Category: Stan, C A.]]
		+	[[Category: Tran, R.]]
		+	[[Category: Uhlig, J.]]
		+	[[Category: Weng, T C.]]
		+	[[Category: Williams, G J.]]
		+	[[Category: Yachandra, V K.]]
		+	[[Category: Yano, J.]]
		+	[[Category: Zouni, A.]]
		+	[[Category: Zwart, P H.]]
		+	[[Category: Electron transport]]
		+	[[Category: Membrane protein]]
		+	[[Category: Photosynthesis]]
		+	[[Category: Water oxidation]]
		+	[[Category: X-ray free electron laser]]

OCA: Protected "4tnk" [edit=sysop:move=sysop]

2014-06-11T08:14:52Z

Protected "4tnk" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:14, 11 June 2014

OCA: New page: '''Unreleased structure''' The entry 4tnk is ON HOLD Authors: Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., Ibrahim, M., Gul, S., Laksmono, H., Sierra, R.G....

2014-06-11T08:14:51Z

New page: '''Unreleased structure''' The entry 4tnk is ON HOLD Authors: Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., Ibrahim, M., Gul, S., Laksmono, H., Sierra, R.G....

New page

'''Unreleased structure'''

The entry 4tnk is ON HOLD

Authors: Kern, J., Tran, R., Alonso-Mori, R., Koroidov, S., Echols, N., Hattne, J., Ibrahim, M., Gul, S., Laksmono, H., Sierra, R.G., Gildea, R.J., Han, G., Hellmich, J., Lassalle-Kaiser, B., Chatterjee, R., Brewster, A., Stan, C.A., Gloeckner, C., Lampe, A., DiFiore, D., Milathianaki, D., Fry, A.R., Seibert, M.M., Koglin, J.E., Gallo, E., Uhlig, J., Sokaras, D., Weng, T.-C., Zwart, P.H., Skinner, D.E., Bogan, M.J., Messerschmidt, M., Glatzel, P., Williams, G.J., Boutet, S., Adams, P.D., Zouni, A., Messinger, J., Sauter, N.K., Bergmann, U., Yano, J., Yachandra, V.K.

Description: RT XFEL structure of Photosystem II 250 microsec after the third illumination at 5.2 A resolution