6op4 - Revision history

OCA at 07:14, 11 October 2023

OCA — Wed, 11 Oct 2023 07:14:35 GMT

←Older revision		Revision as of 07:14, 11 October 2023
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	<StructureSection load='6op4' size='340' side='right'caption='[[6op4]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6op4' size='340' side='right'caption='[[6op4]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6op4]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OP4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6OP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6op4]] 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=6OP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OP4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</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>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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='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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</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>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6op4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op4 OCA], [~~http~~://pdbe.org/6op4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6op4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6op4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6op4 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=6op4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op4 OCA], [https://pdbe.org/6op4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6op4 RCSB], [https://www.ebi.ac.uk/pdbsum/6op4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6op4 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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	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nitrogenase]]~~	+	[[Category: Arias RJ]]
-	[[Category: Arias~~, R J~~]]	+	[[Category: Rees DC]]
-	[[Category: Rees~~, D C]]~~	+
-	~~[[Category: Carbon monoxide]]~~	+
-	~~[[Category: Femo-cofactor]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Selenium~~]]	+

OCA at 11:55, 1 January 2020

OCA — Wed, 01 Jan 2020 11:55:38 GMT

←Older revision		Revision as of 11:55, 1 January 2020
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	</div>		</div>
	<div class="pdbe-citations 6op4" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6op4" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:41, 14 August 2019

OCA — Wed, 14 Aug 2019 16:41:52 GMT

←Older revision		Revision as of 16:41, 14 August 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6op4 is ~~ON HOLD until Paper~~ Publication	+	==Selenium-incorporated, carbon monoxide-inhibited, reactivated FeMo-cofactor of nitrogenase from Azotobacter vinelandii==
		+	<StructureSection load='6op4' size='340' side='right'caption='[[6op4]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6op4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6OP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6OP4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</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>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=6op4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6op4 OCA], [http://pdbe.org/6op4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6op4 RCSB], [http://www.ebi.ac.uk/pdbsum/6op4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6op4 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 ==
		+	The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongo-ing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se in-teractions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscop-ic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assign-ment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and struc-tural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.

-	~~Authors:~~ Arias, ~~R.J.~~, ~~Rees~~, D.C.	+	Localized Electronic Structure of Nitrogenase FeMoco Re-vealed by Selenium K-edge High Resolution X-ray Absorption Spectroscopy.,Henthorn JT, Arias RJ, Koroidov S, Kroll T, Sokaras D, Bergmann U, Rees DC, DeBeer S J Am Chem Soc. 2019 Jul 29. doi: 10.1021/jacs.9b06988. PMID:31356071<ref>PMID:31356071</ref>

-	~~Description: Selenium-incorporated~~, ~~carbon monoxide~~-~~inhibited, reactivated FeMo~~-~~cofactor of nitrogenase from~~ Azotobacter vinelandii	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Rees, D.C~~]]	+	<div class="pdbe-citations 6op4" style="background-color:#fffaf0;"></div>
-	[[Category: Arias, R.J]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Azotobacter vinelandii]]
		+	[[Category: Large Structures]]
		+	[[Category: Nitrogenase]]
		+	[[Category: Arias, R J]]
		+	[[Category: Rees, D C]]
		+	[[Category: Carbon monoxide]]
		+	[[Category: Femo-cofactor]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Selenium]]

OCA at 21:05, 5 June 2019

OCA — Wed, 05 Jun 2019 21:05:54 GMT

←Older revision		Revision as of 21:05, 5 June 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6op4 is ON HOLD	+	The entry 6op4 is ON HOLD until Paper Publication

	Authors: Arias, R.J., Rees, D.C.		Authors: Arias, R.J., Rees, D.C.

OCA: Protected "6op4" [edit=sysop:move=sysop]

OCA — Wed, 01 May 2019 07:16:15 GMT

Protected "6op4" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:16, 1 May 2019

OCA: New page: '''Unreleased structure''' The entry 6op4 is ON HOLD Authors: Arias, R.J., Rees, D.C. Description: Selenium-incorporated, carbon monoxide-inhibited, reactivated FeMo-cofactor of nitrog...

OCA — Wed, 01 May 2019 07:16:14 GMT

New page: '''Unreleased structure''' The entry 6op4 is ON HOLD Authors: Arias, R.J., Rees, D.C. Description: Selenium-incorporated, carbon monoxide-inhibited, reactivated FeMo-cofactor of nitrog...

New page

'''Unreleased structure'''

The entry 6op4 is ON HOLD

Authors: Arias, R.J., Rees, D.C.

Description: Selenium-incorporated, carbon monoxide-inhibited, reactivated FeMo-cofactor of nitrogenase from Azotobacter vinelandii
[[Category: Unreleased Structures]]
[[Category: Rees, D.C]]
[[Category: Arias, R.J]]