1dv6 - Revision history

OCA at 06:59, 7 February 2024

OCA — Wed, 07 Feb 2024 06:59:39 GMT

←Older revision		Revision as of 06:59, 7 February 2024
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	<StructureSection load='1dv6' size='340' side='right'caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1dv6' size='340' side='right'caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Rhodobacter_sphaeroides Rhodobacter~~ sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [https://pdbe.org/1dv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv6 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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [https://pdbe.org/1dv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RCEL_RHOSH RCEL_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[https://www.uniprot.org/uniprot/RCEH_RHOSH RCEH_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[https://www.uniprot.org/uniprot/RCEM_RHOSH RCEM_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.	+	[https://www.uniprot.org/uniprot/RCEL_CERSP RCEL_CERSP] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dv6 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dv6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The reaction center (RC) from Rhodobacter sphaeroides couples light-driven electron transfer to protonation of a bound quinone acceptor molecule, Q(B), within the RC. The binding of Cd(2+) or Zn(2+) has been previously shown to inhibit the rate of reduction and protonation of Q(B). We report here on the metal binding site, determined by x-ray diffraction at 2.5-A resolution, obtained from RC crystals that were soaked in the presence of the metal. The structures were refined to R factors of 23% and 24% for the Cd(2+) and Zn(2+) complexes, respectively. Both metals bind to the same location, coordinating to Asp-H124, His-H126, and His-H128. The rate of electron transfer from Q(A)(-) to Q(B) was measured in the Cd(2+)-soaked crystal and found to be the same as in solution in the presence of Cd(2+). In addition to the changes in the kinetics, a structural effect of Cd(2+) on Glu-H173 was observed. This residue was well resolved in the x-ray structure-i.e., ordered-with Cd(2+) bound to the RC, in contrast to its disordered state in the absence of Cd(2+), which suggests that the mobility of Glu-H173 plays an important role in the rate of reduction of Q(B). The position of the Cd(2+) and Zn(2+) localizes the proton entry into the RC near Asp-H124, His-H126, and His-H128. Based on the location of the metal, likely pathways of proton transfer from the aqueous surface to Q(B) are proposed.
-
-	Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers.,Axelrod HL, Abresch EC, Paddock ML, Okamura MY, Feher G Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1542-7. PMID:10677497<ref>PMID:10677497</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dv6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cereibacter sphaeroides]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Rhodobacter sphaeroides]]~~	+	[[Category: Abresch EC]]
-	[[Category: Abresch~~, E C~~]]	+	[[Category: Axelrod HL]]
-	[[Category: Axelrod~~, H L~~]]	+	[[Category: Feher G]]
-	[[Category: Feher, G]]	+	[[Category: Okamura MY]]
-	[[Category: Okamura~~, M Y~~]]	+	[[Category: Paddock ML]]
-	[[Category: Paddock~~, M L]]~~	+
-	~~[[Category: Bacterial photosynthesis]]~~	+
-	~~[[Category: Cation binding]]~~	+
-	~~[[Category: Integral membrane protein]]~~	+
-	~~[[Category: Metal ion binding]]~~	+
-	~~[[Category: Photosynthesis]]~~	+
-	~~[[Category: Proton transfer]]~~	+
-	~~[[Category: Rhodobacter sphaeroide~~]]	+

OCA at 09:31, 21 July 2021

OCA — Wed, 21 Jul 2021 09:31:45 GMT

←Older revision		Revision as of 09:31, 21 July 2021
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	<StructureSection load='1dv6' size='340' side='right'caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1dv6' size='340' side='right'caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</div></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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [~~http~~://pdbe.org/1dv6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dv6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv6 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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [https://pdbe.org/1dv6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dv6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RCEL_RHOSH RCEL_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[~~http~~://www.uniprot.org/uniprot/RCEH_RHOSH RCEH_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[~~http~~://www.uniprot.org/uniprot/RCEM_RHOSH RCEM_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.	+	[[https://www.uniprot.org/uniprot/RCEL_RHOSH RCEL_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[https://www.uniprot.org/uniprot/RCEH_RHOSH RCEH_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[https://www.uniprot.org/uniprot/RCEM_RHOSH RCEM_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:40, 16 October 2019

OCA — Wed, 16 Oct 2019 11:40:13 GMT

←Older revision		Revision as of 11:40, 16 October 2019
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	==PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+==		==PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+==
-	<StructureSection load='1dv6' size='340' side='right' caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1dv6' size='340' side='right'caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	[[Category: Abresch, E C]]		[[Category: Abresch, E C]]

OCA at 07:46, 13 December 2017

OCA — Wed, 13 Dec 2017 07:46:52 GMT

←Older revision		Revision as of 07:46, 13 December 2017
Line 1:		Line 1:
		+
	==PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+==		==PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+==
	<StructureSection load='1dv6' size='340' side='right' caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1dv6' size='340' side='right' caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://pdbe.org/1dv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://pdbe.org/1dv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dv6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/1dv6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/1dv6_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 00:58, 8 February 2016

OCA — Mon, 08 Feb 2016 00:58:03 GMT

←Older revision		Revision as of 00:58, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1dv6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:24, 10 September 2015

OCA — Thu, 10 Sep 2015 06:24:01 GMT

←Older revision		Revision as of 06:24, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://pdbe.org/1dv6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1dv6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:24, 24 December 2014

OCA — Wed, 24 Dec 2014 19:24:28 GMT

←Older revision		Revision as of 19:24, 24 December 2014
Line 7:		Line 7:
	<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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RCEL_RHOSH RCEL_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/RCEH_RHOSH RCEH_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/RCEM_RHOSH RCEM_RHOSH]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 21:20, 22 December 2014

OCA — Mon, 22 Dec 2014 21:20:28 GMT

←Older revision		Revision as of 21:20, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
-	[[Category: Abresch, E C.]]	+	[[Category: Abresch, E C]]
-	[[Category: Axelrod, H L.]]	+	[[Category: Axelrod, H L]]
-	[[Category: Feher, G.]]	+	[[Category: Feher, G]]
-	[[Category: Okamura, M Y.]]	+	[[Category: Okamura, M Y]]
-	[[Category: Paddock, M L.]]	+	[[Category: Paddock, M L]]
	[[Category: Bacterial photosynthesis]]		[[Category: Bacterial photosynthesis]]
	[[Category: Cation binding]]		[[Category: Cation binding]]

OCA at 10:34, 10 September 2014

OCA — Wed, 10 Sep 2014 10:34:47 GMT

←Older revision		Revision as of 10:34, 10 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1dv6.~~png~~\|~~left~~\|200px]]	+	==PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+==
		+	<StructureSection load='1dv6' size='340' side='right' caption='[[1dv6]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dv6]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DV6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCL:BACTERIOCHLOROPHYLL+A'>BCL</scene>, <scene name='pdbligand=BPH:BACTERIOPHEOPHYTIN+A'>BPH</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=U10:UBIQUINONE-10'>U10</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aij\|1aij]], [[1ds8\|1ds8]], [[1dv3\|1dv3]]</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=1dv6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dv6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dv6 RCSB], [http://www.ebi.ac.uk/pdbsum/1dv6 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dv/1dv6_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The reaction center (RC) from Rhodobacter sphaeroides couples light-driven electron transfer to protonation of a bound quinone acceptor molecule, Q(B), within the RC. The binding of Cd(2+) or Zn(2+) has been previously shown to inhibit the rate of reduction and protonation of Q(B). We report here on the metal binding site, determined by x-ray diffraction at 2.5-A resolution, obtained from RC crystals that were soaked in the presence of the metal. The structures were refined to R factors of 23% and 24% for the Cd(2+) and Zn(2+) complexes, respectively. Both metals bind to the same location, coordinating to Asp-H124, His-H126, and His-H128. The rate of electron transfer from Q(A)(-) to Q(B) was measured in the Cd(2+)-soaked crystal and found to be the same as in solution in the presence of Cd(2+). In addition to the changes in the kinetics, a structural effect of Cd(2+) on Glu-H173 was observed. This residue was well resolved in the x-ray structure-i.e., ordered-with Cd(2+) bound to the RC, in contrast to its disordered state in the absence of Cd(2+), which suggests that the mobility of Glu-H173 plays an important role in the rate of reduction of Q(B). The position of the Cd(2+) and Zn(2+) localizes the proton entry into the RC near Asp-H124, His-H126, and His-H128. Based on the location of the metal, likely pathways of proton transfer from the aqueous surface to Q(B) are proposed.

-	~~{{STRUCTURE_1dv6\| PDB=1dv6 \| SCENE= }}~~	+	Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers.,Axelrod HL, Abresch EC, Paddock ML, Okamura MY, Feher G Proc Natl Acad Sci U S A. 2000 Feb 15;97(4):1542-7. PMID:10677497<ref>PMID:10677497</ref>

-	~~===PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR ZN2+===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10677497}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1dv6]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DV6 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010677497<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	[[Category: Abresch, E C.]]		[[Category: Abresch, E C.]]

OCA: Protected "1dv6" [edit=sysop:move=sysop]

OCA — Wed, 31 Oct 2012 09:47:46 GMT

Protected "1dv6" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:47, 31 October 2012