6n4j - Revision history

OCA at 06:44, 11 October 2023

OCA — Wed, 11 Oct 2023 06:44:52 GMT

←Older revision		Revision as of 06:44, 11 October 2023
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	<StructureSection load='6n4j' size='340' side='right'caption='[[6n4j]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6n4j' size='340' side='right'caption='[[6n4j]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n4j]] is a 2 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=6N4J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n4j]] is a 2 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=6N4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N4J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.95Å</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=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6n4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4j OCA], [~~http~~://pdbe.org/6n4j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n4j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n4j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4j 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=6n4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4j OCA], [https://pdbe.org/6n4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n4j RCSB], [https://www.ebi.ac.uk/pdbsum/6n4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533]	+	[https://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533]
	<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: Rees DC]]
-	[[Category: Rees~~, D C~~]]	+	[[Category: Spatzal T]]
-	[[Category: Spatzal, T]]	+	[[Category: Wenke BB]]
-	[[Category: Wenke~~, B B]]~~	+
-	~~[[Category: Iron sulfur cluster]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:34, 1 January 2020

OCA — Wed, 01 Jan 2020 11:34:11 GMT

←Older revision		Revision as of 11:34, 1 January 2020
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	</div>		</div>
	<div class="pdbe-citations 6n4j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6n4j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nitrogenase 3D structures\|Nitrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:08, 27 March 2019

OCA — Wed, 27 Mar 2019 07:08:46 GMT

←Older revision		Revision as of 07:08, 27 March 2019
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	==Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii==		==Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii==
-	<StructureSection load='6n4j' size='340' side='right' caption='[[6n4j]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='6n4j' size='340' side='right'caption='[[6n4j]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6n4j]] is a 2 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=6N4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4J FirstGlance]. <br>		<table><tr><td colspan='2'>[[6n4j]] is a 2 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=6N4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4J FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
		+	[[Category: Large Structures]]
	[[Category: Nitrogenase]]		[[Category: Nitrogenase]]
	[[Category: Rees, D C]]		[[Category: Rees, D C]]

OCA at 09:36, 13 February 2019

OCA — Wed, 13 Feb 2019 09:36:13 GMT

←Older revision		Revision as of 09:36, 13 February 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6n4j is ~~ON HOLD until Paper~~ Publication	+	==Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii==
		+	<StructureSection load='6n4j' size='340' side='right' caption='[[6n4j]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n4j]] is a 2 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=6N4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N4J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=6n4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n4j OCA], [http://pdbe.org/6n4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n4j RCSB], [http://www.ebi.ac.uk/pdbsum/6n4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n4j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NIFH1_AZOVI NIFH1_AZOVI]] The key enzymatic reactions in nitrogen fixation are catalyzed by the nitrogenase complex, which has 2 components: the iron protein (component 2) and a component 1 which is either a molybdenum-iron protein, a vanadium-iron, or an iron-iron protein.[HAMAP-Rule:MF_00533]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nitrogenase iron protein (Fe-protein) serves as the electron donor for biological nitrogen fixation. Understanding how the Fe-protein controls electron transfer to the active site is critical in addressing the mechanism of substrate reduction. The Fe-protein contains an unusual [4Fe:4S] iron-sulphur cluster that is stable in three oxidation states: 2+, 1+ and 0. Here, we combine structural and spectroscopic techniques, including spatially resolved anomalous dispersion refinement (SpReAD), to report oxidation assignments for individual irons in the cluster for each overall state. Additionally, we report the 1.13-A resolution structure for the Fe-protein with bound ADP, the highest resolution Fe-protein structure presently determined. In the dithionite-reduced [4Fe:4S]1+ state, the SpReAD analysis supports the oxidation state assignment of a delocalized Fe2.5+ pair and a reduced Fe2+ pair. Our work identifies the Fe2.5+ pair as coordinated by the solvent exposed Cys97, while the Fe2+ pair faces the protein interior and is coordinated by Cys132. It is proposed that binding of ATP to the Fe-protein promotes an internal redox rearrangement such that the solvent-exposed Fe becomes reduced, thereby facilitating electron transfer to the nitrogenase molybdenum iron-protein. The SpReAD analysis supports a uniform oxidation state assignment of Fe2+ for all irons in the titanium citrate-reduced [4Fe:4S]0 state, while all irons in the IDS oxidized [4Fe:4S]2+ state are assigned to the valence delocalized Fe2.5+ state.

-	~~Authors~~: ~~Wenke, B.B~~., ~~Spatzal~~, T., Rees~~, D~~.C.	+	Site-specific oxidation state assignments of the irons in the [4Fe:4S]2+/1+/0 states of the nitrogenase Fe-protein.,Wenke BB, Spatzal T, Rees DC Angew Chem Int Ed Engl. 2019 Jan 30. doi: 10.1002/anie.201813966. PMID:30698901<ref>PMID:30698901</ref>

-	~~Description: Ti(III)citrate-reduced~~, ~~nucleotide-free form~~ of the ~~nitrogenase Fe-protein from A~~. vinelandii	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6n4j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Azotobacter vinelandii]]
		+	[[Category: Nitrogenase]]
		+	[[Category: Rees, D C]]
	[[Category: Spatzal, T]]		[[Category: Spatzal, T]]
-	[[Category: ~~Rees~~, ~~D.C~~]]	+	[[Category: Wenke, B B]]
-	[[Category: ~~Wenke, B.B~~]]	+	[[Category: Iron sulfur cluster]]
		+	[[Category: Oxidoreductase]]

OCA at 05:19, 12 December 2018

OCA — Wed, 12 Dec 2018 05:19:45 GMT

←Older revision		Revision as of 05:19, 12 December 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n4j is ON HOLD	+	The entry 6n4j is ON HOLD until Paper Publication

	Authors: Wenke, B.B., Spatzal, T., Rees, D.C.		Authors: Wenke, B.B., Spatzal, T., Rees, D.C.
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	Description: Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii		Description: Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Spatzal, T]]
	[[Category: Rees, D.C]]		[[Category: Rees, D.C]]
	[[Category: Wenke, B.B]]		[[Category: Wenke, B.B]]
-	[[Category: Spatzal, T]]

OCA: Protected "6n4j" [edit=sysop:move=sysop]

OCA — Sun, 02 Dec 2018 19:15:49 GMT

Protected "6n4j" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:15, 2 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n4j is ON HOLD Authors: Wenke, B.B., Spatzal, T., Rees, D.C. Description: Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-prote...

OCA — Sun, 02 Dec 2018 19:15:47 GMT

New page: '''Unreleased structure''' The entry 6n4j is ON HOLD Authors: Wenke, B.B., Spatzal, T., Rees, D.C. Description: Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-prote...

New page

'''Unreleased structure'''

The entry 6n4j is ON HOLD

Authors: Wenke, B.B., Spatzal, T., Rees, D.C.

Description: Ti(III)citrate-reduced, nucleotide-free form of the nitrogenase Fe-protein from A. vinelandii
[[Category: Unreleased Structures]]
[[Category: Rees, D.C]]
[[Category: Wenke, B.B]]
[[Category: Spatzal, T]]