5vpw - Revision history

OCA at 13:54, 4 October 2023

OCA — Wed, 04 Oct 2023 13:54:56 GMT

←Older revision		Revision as of 13:54, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5vpw' size='340' side='right'caption='[[5vpw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5vpw' size='340' side='right'caption='[[5vpw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vpw]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_pasteurianus"_(winogradsky_1895)_lehmann_and_neumann_1907 "bacillus pasteurianus" (winogradsky 1895) lehmann and neumann 1907~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VPW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vpw]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_pasteurianum Clostridium pasteurianum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VPW 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=FE2:FE+(II)+ION'>FE2</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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vq3\|5vq3]], [[5vq4\|5vq4]]</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=FE2:FE+(II)+ION'>FE2</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=1501 "Bacillus pasteurianus" (Winogradsky 1895) Lehmann and Neumann 1907]), nifK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1501 "Bacillus pasteurianus" (Winogradsky 1895) Lehmann and Neumann 1907])</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=5vpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vpw OCA], [https://pdbe.org/5vpw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vpw RCSB], [https://www.ebi.ac.uk/pdbsum/5vpw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vpw 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=5vpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vpw OCA], [~~http~~://pdbe.org/5vpw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vpw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vpw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vpw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NIFD_CLOPA NIFD_CLOPA~~]] 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_CLOPA NIFK_CLOPA]~~] 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_CLOPA NIFD_CLOPA] 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 ==
Line 28:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Clostridium pasteurianum]]
	[[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: Cp1]]~~	+
-	~~[[Category: Mofe protein]]~~	+
-	~~[[Category: Molybdenum-iron protein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:38, 1 January 2020

OCA — Wed, 01 Jan 2020 09:38:05 GMT

←Older revision		Revision as of 09:38, 1 January 2020
Line 1:		Line 1:

	==Nitrogenase Cp1 at pH 5==		==Nitrogenase Cp1 at pH 5==
-	<StructureSection load='5vpw' size='340' side='right' caption='[[5vpw]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5vpw' size='340' side='right'caption='[[5vpw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vpw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pasteurianus"_(winogradsky_1895)_lehmann_and_neumann_1907 "bacillus pasteurianus" (winogradsky 1895) lehmann and neumann 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VPW FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vpw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pasteurianus"_(winogradsky_1895)_lehmann_and_neumann_1907 "bacillus pasteurianus" (winogradsky 1895) lehmann and neumann 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VPW FirstGlance]. <br>
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5vpw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vpw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Morrison, C N]]		[[Category: Morrison, C N]]

OCA at 10:30, 22 November 2017

OCA — Wed, 22 Nov 2017 10:30:29 GMT

←Older revision		Revision as of 10:30, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='5vpw' size='340' side='right' caption='[[5vpw]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5vpw' size='340' side='right' caption='[[5vpw]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vpw]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vpw]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_pasteurianus"_(winogradsky_1895)_lehmann_and_neumann_1907 "bacillus pasteurianus" (winogradsky 1895) lehmann and neumann 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VPW 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=FE2:FE+(II)+ION'>FE2</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=FE2:FE+(II)+ION'>FE2</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">[[5vq3\|5vq3]], [[5vq4\|5vq4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vq3\|5vq3]], [[5vq4\|5vq4]]</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=1501 "Bacillus pasteurianus" (Winogradsky 1895) Lehmann and Neumann 1907]), nifK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1501 "Bacillus pasteurianus" (Winogradsky 1895) Lehmann and Neumann 1907])</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=5vpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vpw OCA], [http://pdbe.org/5vpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vpw RCSB], [http://www.ebi.ac.uk/pdbsum/5vpw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vpw 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=5vpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vpw OCA], [http://pdbe.org/5vpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vpw RCSB], [http://www.ebi.ac.uk/pdbsum/5vpw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vpw ProSAT]</span></td></tr>

OCA at 11:05, 24 August 2017

OCA — Thu, 24 Aug 2017 11:05:39 GMT

←Older revision		Revision as of 11:05, 24 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vpw is ~~ON HOLD~~	+	==Nitrogenase Cp1 at pH 5==
		+	<StructureSection load='5vpw' size='340' side='right' caption='[[5vpw]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5vpw]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VPW 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=FE2:FE+(II)+ION'>FE2</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">[[5vq3\|5vq3]], [[5vq4\|5vq4]]</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=5vpw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vpw OCA], [http://pdbe.org/5vpw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vpw RCSB], [http://www.ebi.ac.uk/pdbsum/5vpw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vpw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NIFD_CLOPA NIFD_CLOPA]] 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_CLOPA NIFK_CLOPA]] 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~~:	+	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~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5vpw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Nitrogenase]]
		+	[[Category: Morrison, C N]]
		+	[[Category: Rees, D C]]
		+	[[Category: Spatzal, T]]
		+	[[Category: Cp1]]
		+	[[Category: Mofe protein]]
		+	[[Category: Molybdenum-iron protein]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 17 May 2017 14:05:54 GMT

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

←Older revision

Revision as of 14:05, 17 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vpw is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 17 May 2017 14:05:52 GMT

New page: '''Unreleased structure''' The entry 5vpw is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vpw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]