5vq4 - Revision history

OCA at 13:55, 4 October 2023

2023-10-04T13:55:00Z

←Older revision		Revision as of 13:55, 4 October 2023
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	<StructureSection load='5vq4' size='340' side='right'caption='[[5vq4]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5vq4' size='340' side='right'caption='[[5vq4]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vq4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_478 Atcc 478~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vq4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vpw\|5vpw]], [[5vq3\|5vq3]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nifD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478]), nifK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478])</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=5vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vq4 OCA], [https://pdbe.org/5vq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vq4 RCSB], [https://www.ebi.ac.uk/pdbsum/5vq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vq4 ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=5vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vq4 OCA], [~~http~~://pdbe.org/5vq4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vq4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vq4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vq4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI~~]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [[http://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_AZOVI]~~] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.	+	[https://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 478~~]]	+	[[Category: Azotobacter vinelandii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nitrogenase]]~~	+	[[Category: Morrison CN]]
-	[[Category: Morrison~~, C N~~]]	+	[[Category: Rees DC]]
-	[[Category: Rees~~, D C~~]]	+	[[Category: Spatzal T]]
-	[[Category: Spatzal, T]]	+
-	~~[[Category: Av1]]~~	+
-	~~[[Category: Mofe protein]]~~	+
-	~~[[Category: Molybdenum-iron protein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:38, 1 January 2020

2020-01-01T09:38:27Z

←Older revision		Revision as of 09:38, 1 January 2020
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	==Nitrogenase Av1 at pH 5==		==Nitrogenase Av1 at pH 5==
-	<StructureSection load='5vq4' size='340' side='right' caption='[[5vq4]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5vq4' size='340' side='right'caption='[[5vq4]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vq4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_478 Atcc 478]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vq4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_478 Atcc 478]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5vq4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vq4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 478]]		[[Category: Atcc 478]]
		+	[[Category: Large Structures]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Morrison, C N]]		[[Category: Morrison, C N]]

OCA at 10:30, 22 November 2017

2017-11-22T10:30:43Z

←Older revision		Revision as of 10:30, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='5vq4' size='340' side='right' caption='[[5vq4]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5vq4' size='340' side='right' caption='[[5vq4]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vq4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vq4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_478 Atcc 478]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vpw\|5vpw]], [[5vq3\|5vq3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vpw\|5vpw]], [[5vq3\|5vq3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nifD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478]), nifK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=354 ATCC 478])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=5vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vq4 OCA], [http://pdbe.org/5vq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vq4 RCSB], [http://www.ebi.ac.uk/pdbsum/5vq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vq4 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=5vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vq4 OCA], [http://pdbe.org/5vq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vq4 RCSB], [http://www.ebi.ac.uk/pdbsum/5vq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vq4 ProSAT]</span></td></tr>
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 478]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Morrison, C N]]		[[Category: Morrison, C N]]

OCA at 11:00, 24 August 2017

2017-08-24T11:00:06Z

←Older revision		Revision as of 11:00, 24 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vq4 is ~~ON HOLD~~	+	==Nitrogenase Av1 at pH 5==
		+	<StructureSection load='5vq4' size='340' side='right' caption='[[5vq4]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vq4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VQ4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=ICS:IRON-SULFUR-MOLYBDENUM+CLUSTER+WITH+INTERSTITIAL+CARBON'>ICS</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vpw\|5vpw]], [[5vq3\|5vq3]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </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=5vq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vq4 OCA], [http://pdbe.org/5vq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vq4 RCSB], [http://www.ebi.ac.uk/pdbsum/5vq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vq4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NIFD_AZOVI NIFD_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation. [[http://www.uniprot.org/uniprot/NIFK_AZOVI NIFK_AZOVI]] This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Protonated states of the nitrogenase active site are mechanistically significant since substrate reduction is invariably accompanied by proton uptake. We report the low pH characterization by X-ray crystallography and EPR spectroscopy of the nitrogenase molybdenum iron (MoFe) proteins from two phylogenetically distinct nitrogenases (Azotobacter vinelandii, Av, and Clostridium pasteurianum, Cp) at pHs between 4.5 and 8. X-ray data at pHs of 4.5-6 reveal the repositioning of side chains along one side of the FeMo-cofactor, and the corresponding EPR data shows a new S = 3/2 spin system with spectral features similar to a state previously observed during catalytic turnover. The structural changes suggest that FeMo-cofactor belt sulfurs S3A or S5A are potential protonation sites. Notably, the observed structural and electronic low pH changes are correlated and reversible. The detailed structural rearrangements differ between the two MoFe proteins, which may reflect differences in potential protonation sites at the active site among nitrogenase species. These observations emphasize the benefits of investigating multiple nitrogenase species. Our experimental data suggest that reversible protonation of the resting state is likely occurring, and we term this state "E0H+", following the Lowe-Thorneley naming scheme.

-	~~Authors: Morrison, C.N~~., ~~Spatzal~~, T., Rees~~, D~~.C.	+	Reversible Protonated Resting State of the Nitrogenase Active Site.,Morrison CN, Spatzal T, Rees DC J Am Chem Soc. 2017 Aug 9;139(31):10856-10862. doi: 10.1021/jacs.7b05695. Epub, 2017 Jul 26. PMID:28692802<ref>PMID:28692802</ref>

-	~~Description~~: ~~Nitrogenase Av1 at pH 5~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Morrison, C.N]]	+	<div class="pdbe-citations 5vq4" style="background-color:#fffaf0;"></div>
-	[[Category: Rees, D.C]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Nitrogenase]]
		+	[[Category: Morrison, C N]]
		+	[[Category: Rees, D C]]
	[[Category: Spatzal, T]]		[[Category: Spatzal, T]]
		+	[[Category: Av1]]
		+	[[Category: Mofe protein]]
		+	[[Category: Molybdenum-iron protein]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "5vq4" [edit=sysop:move=sysop]

2017-05-17T14:06:21Z

Protected "5vq4" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:06, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vq4 is ON HOLD Authors: Morrison, C.N., Spatzal, T., Rees, D.C. Description: Nitrogenase Av1 at pH 5 Category: Unreleased Structures [[Categor...

2017-05-17T14:06:20Z

New page: '''Unreleased structure''' The entry 5vq4 is ON HOLD Authors: Morrison, C.N., Spatzal, T., Rees, D.C. Description: Nitrogenase Av1 at pH 5 Category: Unreleased Structures [[Categor...

New page

'''Unreleased structure'''

The entry 5vq4 is ON HOLD

Authors: Morrison, C.N., Spatzal, T., Rees, D.C.

Description: Nitrogenase Av1 at pH 5
[[Category: Unreleased Structures]]
[[Category: Morrison, C.N]]
[[Category: Rees, D.C]]
[[Category: Spatzal, T]]