5auk - Revision history

OCA at 15:48, 8 November 2023

OCA — Wed, 08 Nov 2023 15:48:10 GMT

←Older revision		Revision as of 15:48, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AUK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AUK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GAK:[2GA-2S]+CLUSTER'>GAK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.62Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GAK:[2GA-2S]+CLUSTER'>GAK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5auk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auk OCA], [https://pdbe.org/5auk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5auk RCSB], [https://www.ebi.ac.uk/pdbsum/5auk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5auk 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=5auk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auk OCA], [https://pdbe.org/5auk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5auk RCSB], [https://www.ebi.ac.uk/pdbsum/5auk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5auk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:26, 31 May 2023

OCA — Wed, 31 May 2023 06:26:21 GMT

←Older revision		Revision as of 06:26, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5auk' size='340' side='right'caption='[[5auk]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='5auk' size='340' side='right'caption='[[5auk]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Syny3 Syny3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechocystis_sp._PCC_6803_substr._Kazusa Synechocystis sp. PCC 6803 substr. Kazusa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AUK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GAK:[2GA-2S]+CLUSTER'>GAK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GAK:[2GA-2S]+CLUSTER'>GAK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aui\|5aui]]</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=5auk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auk OCA], [https://pdbe.org/5auk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5auk RCSB], [https://www.ebi.ac.uk/pdbsum/5auk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5auk ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">petF, fed ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1111708 SYNY3])~~</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=5auk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auk OCA], [~~http~~://pdbe.org/5auk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5auk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5auk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5auk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FER_SYNY3 FER_SYNY3]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.	+	[https://www.uniprot.org/uniprot/FER_SYNY3 FER_SYNY3] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Syny3~~]]	+	[[Category: Synechocystis sp. PCC 6803 substr. Kazusa]]
-	[[Category: Hase, T]]	+	[[Category: Hase T]]
-	[[Category: Kurisu, G]]	+	[[Category: Kurisu G]]
-	[[Category: Muraki, N]]	+	[[Category: Muraki N]]
-	[[Category: Taya, M]]	+	[[Category: Taya M]]
-	~~[[Category: Analogue]]~~	+
-	~~[[Category: Electron transfer protein]]~~	+
-	~~[[Category: Electron transport~~]]	+

OCA at 07:06, 19 February 2020

OCA — Wed, 19 Feb 2020 07:06:25 GMT

←Older revision		Revision as of 07:06, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of the Ga-substituted Ferredoxin==		==Crystal structure of the Ga-substituted Ferredoxin==
-	<StructureSection load='5auk' size='340' side='right' caption='[[5auk]], [[Resolution\|resolution]] 1.62Å' scene=''>	+	<StructureSection load='5auk' size='340' side='right'caption='[[5auk]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUK FirstGlance]. <br>		<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUK FirstGlance]. <br>
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5auk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5auk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ferredoxin 3D structures\|Ferredoxin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Syny3]]		[[Category: Syny3]]
	[[Category: Hase, T]]		[[Category: Hase, T]]

OCA at 15:39, 16 November 2017

OCA — Thu, 16 Nov 2017 15:39:35 GMT

←Older revision		Revision as of 15:39, 16 November 2017
Line 1:		Line 1:
		+
	==Crystal structure of the Ga-substituted Ferredoxin==		==Crystal structure of the Ga-substituted Ferredoxin==
	<StructureSection load='5auk' size='340' side='right' caption='[[5auk]], [[Resolution\|resolution]] 1.62Å' scene=''>		<StructureSection load='5auk' size='340' side='right' caption='[[5auk]], [[Resolution\|resolution]] 1.62Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Syny3 Syny3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GAK:[2GA-2S]+CLUSTER'>GAK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GAK:[2GA-2S]+CLUSTER'>GAK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aui\|5aui]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aui\|5aui]]</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=5auk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auk OCA], [http://pdbe.org/5auk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5auk RCSB], [http://www.ebi.ac.uk/pdbsum/5auk PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">petF, fed ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1111708 SYNY3])</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=5auk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auk OCA], [http://pdbe.org/5auk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5auk RCSB], [http://www.ebi.ac.uk/pdbsum/5auk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5auk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Syny3]]
	[[Category: Hase, T]]		[[Category: Hase, T]]
	[[Category: Kurisu, G]]		[[Category: Kurisu, G]]
Line 28:		Line 31:
	[[Category: Analogue]]		[[Category: Analogue]]
	[[Category: Electron transfer protein]]		[[Category: Electron transfer protein]]
		+	[[Category: Electron transport]]

OCA at 21:50, 15 October 2015

OCA — Thu, 15 Oct 2015 21:50:13 GMT

←Older revision		Revision as of 21:50, 15 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of the Ga-substituted Ferredoxin==
		+	<StructureSection load='5auk' size='340' side='right' caption='[[5auk]], [[Resolution\|resolution]] 1.62Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5auk]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AUK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BEN:BENZAMIDINE'>BEN</scene>, <scene name='pdbligand=GAK:[2GA-2S]+CLUSTER'>GAK</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5aui\|5aui]]</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=5auk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5auk OCA], [http://pdbe.org/5auk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5auk RCSB], [http://www.ebi.ac.uk/pdbsum/5auk PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FER_SYNY3 FER_SYNY3]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In chloroplasts, ferredoxin (Fd) is reduced by Photosystem I (PSI) and oxidized by Fd-NADP(+) reductase (FNR) that is involved in NADP(+) reduction. To understand the structural basis for the dynamics and efficiency of the electron transfer reaction via Fd, we complementary used X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. In the NMR analysis of the formed electron transfer complex with Fd, the paramagnetic effect of the [2Fe-2S] cluster of Fd prevented us from detecting the NMR signals around the cluster. To solve this problem, the paramagnetic iron-sulfur cluster was replaced with a diamagnetic metal cluster. We determined the crystal structure of the Ga-substituted Fd (GaFd) from Synechocystis sp. PCC6803 at 1.62 A resolution and verified its functional complementation using affinity chromatography. NMR analysis of the interaction sites on GaFd with PSI (molecular mass of approximately 1 MDa) and FNR from Thermosynechococcus elongatus was achieved with high-field NMR spectroscopy. With reference to the interaction sites with FNR of Anabaena sp. PCC 7119 from the published crystal data, the interaction sites of Fd with FNR and PSI in solution can be classified into two types: (1) the core hydrophobic residues in the proximity of the metal center and (2) the hydrophilic residues surrounding the core. The former sites are shared in the Fd:FNR and Fd:PSI complex, while the latter ones are target-specific and not conserved on the residual level.

-	~~The entry 5auk is ON HOLD until Paper Publication~~	+	X-ray Structure and Nuclear Magnetic Resonance Analysis of the Interaction Sites of the Ga-Substituted Cyanobacterial Ferredoxin.,Mutoh R, Muraki N, Shinmura K, Kubota-Kawai H, Lee YH, Nowaczyk MM, Rogner M, Hase T, Ikegami T, Kurisu G Biochemistry. 2015 Oct 6;54(39):6052-61. doi: 10.1021/acs.biochem.5b00601. Epub, 2015 Sep 30. PMID:26348494<ref>PMID:26348494</ref>

-	~~Authors: Kurisu~~, G.~~, Muraki, N~~.~~, Taya, M~~., Hase, T.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 5auk" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hase, T]]
		+	[[Category: Kurisu, G]]
		+	[[Category: Muraki, N]]
	[[Category: Taya, M]]		[[Category: Taya, M]]
-	[[Category: ~~Muraki, N~~]]	+	[[Category: Analogue]]
-	[[Category: ~~Kurisu, G]]~~	+	[[Category: Electron transfer protein]]
-	~~[[Category: Hase, T~~]]	+

OCA at 11:29, 13 May 2015

OCA — Wed, 13 May 2015 11:29:43 GMT

←Older revision		Revision as of 11:29, 13 May 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5auk is ON HOLD	+	The entry 5auk is ON HOLD until Paper Publication

	Authors: Kurisu, G., Muraki, N., Taya, M., Hase, T.		Authors: Kurisu, G., Muraki, N., Taya, M., Hase, T.

OCA: Protected "5auk" [edit=sysop:move=sysop]

OCA — Thu, 30 Apr 2015 10:39:01 GMT

Protected "5auk" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:39, 30 April 2015

OCA: New page: '''Unreleased structure''' The entry 5auk is ON HOLD Authors: Kurisu, G., Muraki, N., Taya, M., Hase, T. Description: Category: Unreleased Structures Category: Taya, M [[Categ...

OCA — Thu, 30 Apr 2015 10:39:00 GMT

New page: '''Unreleased structure''' The entry 5auk is ON HOLD Authors: Kurisu, G., Muraki, N., Taya, M., Hase, T. Description: Category: Unreleased Structures Category: Taya, M [[Categ...

New page

'''Unreleased structure'''

The entry 5auk is ON HOLD

Authors: Kurisu, G., Muraki, N., Taya, M., Hase, T.

Description:
[[Category: Unreleased Structures]]
[[Category: Taya, M]]
[[Category: Muraki, N]]
[[Category: Kurisu, G]]
[[Category: Hase, T]]