6fdr - Revision history

OCA at 18:08, 20 September 2023

OCA — Wed, 20 Sep 2023 18:08:58 GMT

←Older revision		Revision as of 18:08, 20 September 2023
Line 1:		Line 1:

	==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A==		==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A==
-	<StructureSection load='6fdr' size='340' side='right' caption='[[6fdr]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='6fdr' size='340' side='right'caption='[[6fdr]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6fdr]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6FDR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6fdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FDR 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=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]] 1.4Å</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=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [~~http~~://pdbe.org/6fdr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6fdr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6fdr 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=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=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [https://pdbe.org/6fdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [https://www.ebi.ac.uk/pdbsum/6fdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fdr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.	+	[https://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 31:

	==See Also==		==See Also==
-	*[[Ferredoxin\|Ferredoxin]]	+	*[[Ferredoxin 3D structures\|Ferredoxin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
-	[[Category: ~~Goodin, D B~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mcree, D E~~]]	+	[[Category: Goodin DB]]
-	[[Category: ~~Schipke, C G~~]]	+	[[Category: Mcree DE]]
-	[[Category: ~~Stout, C D~~]]	+	[[Category: Schipke CG]]
-	[[Category: ~~Electron transport]]~~	+	[[Category: Stout CD]]
-	~~[[Category: Iron-sulfur~~]]	+

OCA at 06:58, 4 April 2018

OCA — Wed, 04 Apr 2018 06:58:33 GMT

←Older revision		Revision as of 06:58, 4 April 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/6fdr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/6fdr_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 00:32, 5 August 2016

OCA — Fri, 05 Aug 2016 00:32:28 GMT

←Older revision		Revision as of 00:32, 5 August 2016
Line 1:		Line 1:
		+
	==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A==		==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A==
	<StructureSection load='6fdr' size='340' side='right' caption='[[6fdr]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6fdr' size='340' side='right' caption='[[6fdr]], [[Resolution\|resolution]] 1.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[6fdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FDR FirstGlance]. <br>		<table><tr><td colspan='2'>[[6fdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FDR 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=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>		</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=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=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [http://www.ebi.ac.uk/pdbsum/6fdr PDBsum]</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=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [http://pdbe.org/6fdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [http://www.ebi.ac.uk/pdbsum/6fdr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fdr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=6fdr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 6fdr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:23, 25 December 2014

OCA — Thu, 25 Dec 2014 14:23:33 GMT

←Older revision		Revision as of 14:23, 25 December 2014
Line 6:		Line 6:
	<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=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [http://www.ebi.ac.uk/pdbsum/6fdr PDBsum]</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=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [http://www.ebi.ac.uk/pdbsum/6fdr PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FER1_AZOVI FER1_AZOVI]] Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions. This ferredoxin could play a role in regulating gene expression by interacting directly with DNA.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:46, 10 December 2014

OCA — Wed, 10 Dec 2014 16:46:06 GMT

←Older revision		Revision as of 16:46, 10 December 2014
Line 1:		Line 1:
-	[[~~Image~~:6fdr.~~png\|left~~\|200px]]	+	==7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A==
		+	<StructureSection load='6fdr' size='340' side='right' caption='[[6fdr]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6fdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FDR 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=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=6fdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fdr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=6fdr RCSB], [http://www.ebi.ac.uk/pdbsum/6fdr PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fd/6fdr_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The refined structure of reduced Azotobacter vinelandii 7Fe ferredoxin FdI at 100 K and 1.4 A resolution is reported, permitting comparison of [3Fe-4S]+ and [3Fe-4S]0 clusters in the same protein at near atomic resolution. The reduced state of the [3Fe-4S]0 cluster is established by single-crystal EPR following data collection. Redundant structures are refined to establish the reproducibility and accuracy of the results for both oxidation states. The structure of the [4Fe-4S]2+ cluster in four independently determined FdI structures is the same within the range of derived standard uncertainties, providing an internal control on the experimental methods and the refinement results. The structures of the [3Fe-4S]+ and [3Fe-4S]0 clusters are also the same within experimental error, indicating that the protein may be enforcing an entatic state upon this cluster, facilitating electron-transfer reactions. The structure of the FdI [3Fe-4S]0 cluster allows direct comparison with the structure of a well-characterized [Fe3S4]0 synthetic analogue compound. The [3Fe-4S]0 cluster displays significant distortions with respect to the [Fe3S4]0 analogue, further suggesting that the observed [3Fe-4S]+/0 geometry in FdI may represent an entatic state. Comparison of oxidized and reduced FdI reveals conformational changes at the protein surface in response to reduction of the [3Fe-4S]+/0 cluster. The carboxyl group of Asp15 rotates approximately 90 degrees, Lys84, a residue hydrogen bonded to Asp15, adopts a single conformation, and additional H2O molecules become ordered. These structural changes imply a mechanism for H+ transfer to the [3Fe-4S]0 cluster in agreement with electrochemical and spectroscopic results.

-	~~{{STRUCTURE_6fdr\| PDB=6fdr \| SCENE= }}~~	+	Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster.,Schipke CG, Goodin DB, McRee DE, Stout CD Biochemistry. 1999 Jun 29;38(26):8228-39. PMID:10387068<ref>PMID:10387068</ref>

-	~~===7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K~~, ~~NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10387068}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[6fdr]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].~~	+

	==See Also==		==See Also==
	*[[Ferredoxin\|Ferredoxin]]		*[[Ferredoxin\|Ferredoxin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010387068<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
-	[[Category: Goodin, D B.]]	+	[[Category: Goodin, D B]]
-	[[Category: Mcree, D E.]]	+	[[Category: Mcree, D E]]
-	[[Category: Schipke, C G.]]	+	[[Category: Schipke, C G]]
-	[[Category: Stout, C D.]]	+	[[Category: Stout, C D]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron-sulfur]]		[[Category: Iron-sulfur]]

OCA at 17:47, 20 October 2012

OCA — Sat, 20 Oct 2012 17:47:02 GMT

←Older revision		Revision as of 17:47, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[6fdr]] is a 1 chain structure ~~of [[Ferredoxin]]~~ with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].	+	[[6fdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].

	==See Also==		==See Also==

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

OCA — Fri, 27 Jul 2012 01:58:38 GMT

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

←Older revision

Revision as of 01:58, 27 July 2012

OCA at 01:58, 27 July 2012

OCA — Fri, 27 Jul 2012 01:58:37 GMT

←Older revision		Revision as of 01:58, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:6fdr.png\|left\|200px]]		[[Image:6fdr.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_6fdr", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_6fdr\| PDB=6fdr \| SCENE= }}		{{STRUCTURE_6fdr\| PDB=6fdr \| SCENE= }}

	===7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A===		===7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_10387068}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 10387068 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_10387068}}		{{ABSTRACT_PUBMED_10387068}}

	==About this Structure==		==About this Structure==
-	~~6FDR~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].	+	[[6fdr]] is a 1 chain structure of [[Ferredoxin]] with sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].
		+
		+	==See Also==
		+	*[[Ferredoxin\|Ferredoxin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~10387068~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:010387068</ref><references group="xtra"/>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
	[[Category: Goodin, D B.]]		[[Category: Goodin, D B.]]
Line 31:		Line 22:
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron-sulfur]]		[[Category: Iron-sulfur]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:36:33 2009''

OCA at 16:36, 17 February 2009

OCA — Tue, 17 Feb 2009 16:36:35 GMT

←Older revision		Revision as of 16:36, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	6FDR is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].	+	6FDR is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Azotobacter_vinelandii Azotobacter vinelandii]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1fdc 1fdc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FDR OCA].

	==Reference==		==Reference==
-	Oxidized and reduced Azotobacter vinelandii ferredoxin I at 1.4 A resolution: conformational change of surface residues without significant change in the [3Fe-4S]+/0 cluster., Schipke CG, Goodin DB, McRee DE, Stout CD, Biochemistry. 1999 Jun 29;38(26):8228-39. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/10387068 10387068]~~	+	<ref group="xtra">PMID:10387068</ref><references group="xtra"/>
	[[Category: Azotobacter vinelandii]]		[[Category: Azotobacter vinelandii]]
-	[[Category: Single protein]]
	[[Category: Goodin, D B.]]		[[Category: Goodin, D B.]]
	[[Category: Mcree, D E.]]		[[Category: Mcree, D E.]]
Line 33:		Line 32:
	[[Category: Iron-sulfur]]		[[Category: Iron-sulfur]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 14:~~18:~~21 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:36:33 2009''

OCA at 11:18, 3 July 2008

OCA — Thu, 03 Jul 2008 11:18:22 GMT

←Older revision		Revision as of 11:18, 3 July 2008
Line 1:		Line 1:
-	[[Image:6fdr.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:6fdr.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_6fdr\| PDB=6fdr \| SCENE= }}		{{STRUCTURE_6fdr\| PDB=6fdr \| SCENE= }}

-	~~'''~~7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A~~'''~~	+	===7-FE FERREDOXIN FROM AZOTOBACTER VINELANDII AT 100K, NA DITHIONITE REDUCED AT PH 8.5, RESOLUTION 1.4 A===


-	~~==Overview==~~	+	<!--
-	~~The refined structure of reduced Azotobacter vinelandii 7Fe ferredoxin FdI at 100 K and 1.4 A resolution is reported, permitting comparison of [3Fe~~-~~4S]+ and [3Fe~~-~~4S]0 clusters in the same protein at near atomic resolution.~~ The reduced state of the [3Fe-4S]0 cluster is established by single-crystal EPR following data collection. Redundant structures are refined to establish the reproducibility and accuracy of the results for both oxidation states. The structure of the [4Fe-4S]2+ cluster in four independently determined FdI structures is the same within the range of derived standard uncertainties, ~~providing an internal control on the experimental methods and the refinement results. The structures of the [3Fe-4S]+ and [3Fe-4S]0 clusters are also the same within experimental error~~, ~~indicating that~~ the protein may be enforcing an entatic state upon this cluster, facilitating electron-transfer reactions. The structure of the FdI [3Fe-4S]0 cluster allows direct comparison with the structure of a well-characterized [Fe3S4]0 synthetic analogue compound. The [3Fe-4S]0 cluster displays significant distortions with respect to the ~~[Fe3S4]0 analogue, further suggesting that the observed [3Fe-4S]+/0 geometry in FdI may represent an entatic state. Comparison of oxidized and reduced FdI reveals conformational changes~~ at ~~the protein surface in response to reduction of the [3Fe-4S]+~~/~~0 cluster~~. ~~The carboxyl group of Asp15 rotates approximately 90 degrees~~, ~~Lys84, a residue hydrogen bonded to Asp15, adopts a single conformation, and additional H2O molecules become ordered~~. ~~These structural changes imply a mechanism for H+ transfer to the [3Fe~~-~~4S]0 cluster in agreement with electrochemical and spectroscopic results.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_10387068}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 10387068 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_10387068}}

	==About this Structure==		==About this Structure==
Line 28:		Line 32:
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron-sulfur]]		[[Category: Iron-sulfur]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:40:20 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 14:18:21 2008''