5xvb - Revision history

OCA at 12:48, 13 August 2026

2026-08-13T12:48:50Z

← Older revision		Revision as of 12:48, 13 August 2026
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5xvb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_sp._S-77 Citrobacter sp. S-77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5xvb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_sp._S-77 Citrobacter sp. S-77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVB FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.84Å</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]] 1.84Å</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat">~~<scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>,~~ <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU~~</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4~~</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</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=5xvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvb OCA], [https://pdbe.org/5xvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvb RCSB], [https://www.ebi.ac.uk/pdbsum/5xvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvb 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=5xvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvb OCA], [https://pdbe.org/5xvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvb RCSB], [https://www.ebi.ac.uk/pdbsum/5xvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/~~A0A3B6UEP7_9ENTR A0A3B6UEP7_9ENTR~~]		[https://www.uniprot.org/uniprot/A0A3B6UEQ0_9ENTR A0A3B6UEQ0_9ENTR] This is one of three E.coli hydrogenases synthesized in response to different physiological conditions. HYD2 is involved in hydrogen uptake.[ARBA:ARBA00059419]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

			Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.,Noor NDM, Matsuura H, Nishikawa K, Tai H, Hirota S, Kim J, Kang J, Tateno M, Yoon KS, Ogo S, Kubota S, Shomura Y, Higuchi Y Chem Commun (Camb). 2018 Oct 30;54(87):12385-12388. doi: 10.1039/c8cc06261g. PMID:30328414<ref>PMID:30328414</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5xvb" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:20, 27 March 2024

2024-03-27T10:20:34Z

← Older revision		Revision as of 10:20, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5xvb' size='340' side='right'caption='[[5xvb]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5xvb' size='340' side='right'caption='[[5xvb]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5xvb]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Citrobacter_sp._s-77 Citrobacter sp. s-77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5xvb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_sp._S-77 Citrobacter sp. S-77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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]] 1.84Å</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=5xvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvb OCA], [~~http~~://pdbe.org/5xvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvb ProSAT]</span></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=5xvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvb OCA], [https://pdbe.org/5xvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvb RCSB], [https://www.ebi.ac.uk/pdbsum/5xvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvb ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~		== Function ==
	== ~~Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/A0A3B6UEP7_9ENTR A0A3B6UEP7_9ENTR]
	Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

	~~Redox-dependent conformational changes of a proximal~~ [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.,Noor NDM, Matsuura H, Nishikawa K, Tai H, Hirota S, Kim J, Kang J, Tateno M, Yoon KS, Ogo S, Kubota S, Shomura Y, Higuchi Y Chem Commun (Camb). 2018 Oct 30;54(87):~~12385-12388. doi: 10.1039~~/~~c8cc06261g. PMID:30328414<ref>PMID:30328414<~~/~~ref>~~

	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~
	</~~div>~~
	~~<div class="pdbe-citations 5xvb" style="background-color:#fffaf0;"><~~/~~div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Citrobacter sp. s-77]]		[[Category: Citrobacter sp. S-77]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi Y]]
	[[Category: Hirota, S]]		[[Category: Hirota S]]
	[[Category: Kang, J]]		[[Category: Kang J]]
	[[Category: Kim, J]]		[[Category: Kim J]]
	[[Category: Matsuura, H]]		[[Category: Matsuura H]]
	[[Category: ~~Nishikawa, K~~]]		[[Category: Muhd Noor ND]]
	[[Category: ~~Noor, N D.Muhd~~]]		[[Category: Nishikawa K]]
	[[Category: Ogo, S]]		[[Category: Ogo S]]
	[[Category: Shomura, Y]]		[[Category: Shomura Y]]
	[[Category: Tai, H]]		[[Category: Tai H]]
	[[Category: Tateno, M]]		[[Category: Tateno M]]
	[[Category: Yoon~~, K S]]~~		[[Category: Yoon KS]]
	~~[[Category: Oxidoreductase~~]]

OCA at 06:14, 10 July 2019

2019-07-10T06:14:25Z

← Older revision		Revision as of 06:14, 10 July 2019
Line 1:		Line 1:

	==[NiFe]-hydrogenase 2 from Citrobacter sp. S-77 in an H2-reduced condition==		==[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition==
	<StructureSection load='5xvb' size='340' side='right' caption='[[5xvb]], [[Resolution\|resolution]] 1.84Å' scene=''>		<StructureSection load='5xvb' size='340' side='right'caption='[[5xvb]], [[Resolution\|resolution]] 1.84Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5xvb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_sp._s-77 Citrobacter sp. s-77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[5xvb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_sp._s-77 Citrobacter sp. s-77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVB FirstGlance]. <br>
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=5xvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvb OCA], [http://pdbe.org/5xvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvb RCSB], [http://www.ebi.ac.uk/pdbsum/5xvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvb ProSAT]</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=5xvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvb OCA], [http://pdbe.org/5xvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvb RCSB], [http://www.ebi.ac.uk/pdbsum/5xvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvb ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

			Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.,Noor NDM, Matsuura H, Nishikawa K, Tai H, Hirota S, Kim J, Kang J, Tateno M, Yoon KS, Ogo S, Kubota S, Shomura Y, Higuchi Y Chem Commun (Camb). 2018 Oct 30;54(87):12385-12388. doi: 10.1039/c8cc06261g. PMID:30328414<ref>PMID:30328414</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5xvb" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Citrobacter sp. s-77]]		[[Category: Citrobacter sp. s-77]]
			[[Category: Large Structures]]
	[[Category: Higuchi, Y]]		[[Category: Higuchi, Y]]
	[[Category: Hirota, S]]		[[Category: Hirota, S]]

OCA at 05:30, 27 June 2018

2018-06-27T05:30:58Z

← Older revision		Revision as of 05:30, 27 June 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 5xvb ~~is ON HOLD until Jun 27 2019~~		==[NiFe]-hydrogenase 2 from Citrobacter sp. S-77 in an H2-reduced condition==
			<StructureSection load='5xvb' size='340' side='right' caption='[[5xvb]], [[Resolution\|resolution]] 1.84Å' scene=''>
	~~Authors~~: ~~Nishikawa, K~~., ~~Matsuura~~, H., ~~Muhd Noor~~, N.D., ~~Tai, H~~., ~~Hirota, S~~., ~~Kim, J~~.~~, Kang, J~~.~~, Tateno, M~~., ~~Yoon, K~~.S.~~, Ogo, S~~., ~~Shomura, Y~~.~~, Higuchi, Y~~.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5xvb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Citrobacter_sp._s-77 Citrobacter sp. s-77]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVB FirstGlance]. <br>
	~~Description~~: ~~[NiFe]-hydrogenase 2 from~~ Citrobacter sp. S-77 ~~in an H2-reduced condition~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NFU:FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)'>NFU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<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=5xvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvb OCA], [http://pdbe.org/5xvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvb RCSB], [http://www.ebi.ac.uk/pdbsum/5xvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvb ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Citrobacter sp. s-77]]
			[[Category: Higuchi, Y]]
			[[Category: Hirota, S]]
	[[Category: Kang, J]]		[[Category: Kang, J]]
			[[Category: Kim, J]]
	[[Category: Matsuura, H]]		[[Category: Matsuura, H]]
	[[Category: Nishikawa, K]]		[[Category: Nishikawa, K]]
	[[Category: ~~Hirota~~, S]]		[[Category: Noor, N D.Muhd]]
	[[Category: ~~Higuchi~~, Y]]		[[Category: Ogo, S]]
	[[Category: ~~Muhd Noor~~, ~~N.D~~]]		[[Category: Shomura, Y]]
	[[Category: Tai, H]]		[[Category: Tai, H]]
	~~[[Category: Yoon, K.S]]~~
	[[Category: Tateno, M]]		[[Category: Tateno, M]]
	[[Category: ~~Kim, J]]~~		[[Category: Yoon, K S]]
	~~[[Category: Ogo~~, S]]		[[Category: Oxidoreductase]]
	[[Category: ~~Shomura, Y~~]]

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

2017-09-27T15:49:11Z

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

← Older revision	Revision as of 15:49, 27 September 2017
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5xvb is ON HOLD until Jun 27 2019 Authors: Nishikawa, K., Matsuura, H., Muhd Noor, N.D., Tai, H., Hirota, S., Kim, J., Kang, J., Tateno, M., Yoon, K...

2017-09-27T15:49:10Z

New page: '''Unreleased structure''' The entry 5xvb is ON HOLD until Jun 27 2019 Authors: Nishikawa, K., Matsuura, H., Muhd Noor, N.D., Tai, H., Hirota, S., Kim, J., Kang, J., Tateno, M., Yoon, K...

New page

'''Unreleased structure'''

The entry 5xvb is ON HOLD until Jun 27 2019

Authors: Nishikawa, K., Matsuura, H., Muhd Noor, N.D., Tai, H., Hirota, S., Kim, J., Kang, J., Tateno, M., Yoon, K.S., Ogo, S., Shomura, Y., Higuchi, Y.

Description: [NiFe]-hydrogenase 2 from Citrobacter sp. S-77 in an H2-reduced condition
[[Category: Unreleased Structures]]
[[Category: Kang, J]]
[[Category: Matsuura, H]]
[[Category: Nishikawa, K]]
[[Category: Hirota, S]]
[[Category: Higuchi, Y]]
[[Category: Muhd Noor, N.D]]
[[Category: Tai, H]]
[[Category: Yoon, K.S]]
[[Category: Tateno, M]]
[[Category: Kim, J]]
[[Category: Ogo, S]]
[[Category: Shomura, Y]]