7rxn - Revision history

OCA at 15:01, 6 March 2024

2024-03-06T15:01:56Z

←Older revision		Revision as of 15:01, 6 March 2024
Line 1:		Line 1:

	==STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION==		==STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION==
-	<StructureSection load='7rxn' size='340' side='right' caption='[[7rxn]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='7rxn' size='340' side='right'caption='[[7rxn]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7rxn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_29579 Atcc 29579~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=7RXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rxn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RXN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.5Å</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=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [~~http~~://pdbe.org/7rxn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7rxn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7rxn ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [https://pdbe.org/7rxn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB], [https://www.ebi.ac.uk/pdbsum/7rxn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rxn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RUBR_DESVH RUBR_DESVH]] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.	+	[https://www.uniprot.org/uniprot/RUBR_DESVH RUBR_DESVH] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/7rxn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/7rxn_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>
Line 19:		Line 20:
	</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=7rxn 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=7rxn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The X-ray model of rubredoxin from Desulfovibrio vulgaris has been refined against 1.5 A X-ray diffraction data collected on a diffractometer. The final model comprises 395 non-hydrogen protein atoms, and 180 solvent O atoms. The final R-value for the model with calculated H atom positions included as fixed contributions is 0.098 over all reflections greater than 2 sigma I from infinity to 1.5 A. The error in co-ordinates is estimated to be 0.08 A. The solvent model was twice redetermined during the later stages of refinement and was instrumental in its success. One sequence error has been detected and corrected (Thr21----Asp). The iron-sulfur site bond angles are distorted from true tetrahedral symmetry, as found in other rubredoxin structures. A significant deviation from tetrahedral angles is seen at C alpha atoms 9, 10, 42 and 43, interior angles of the loops binding the iron atom. The planes of two aromatic groups, Tyr4 and Trp37, are nearly parallel to, and lie under, an extended system of atoms that includes the peptide bonds preceding the first cysteine residue of each cysteine loop as well as the cysteine side-chain, the iron, and the cysteine side-chain of the opposite loop, forming a previously unrecognized extended system that may function in electron transfer.

-	~~Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution.,Adman ET, Sieker LC, Jensen LH J Mol Biol. 1991 Jan 20;217(2):337-52. PMID:1992166<ref>PMID:1992166</ref>~~	+	==See Also==
-		+	*[[Rubredoxin 3D structures\|Rubredoxin 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	*[[Rubredoxin PDB structures\|Rubredoxin PDB structures]]
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 7rxn" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 29579~~]]	+	[[Category: Desulfovibrio vulgaris]]
-	[[Category: Adman~~, E T~~]]	+	[[Category: Large Structures]]
-	[[Category: Jensen~~, L H~~]]	+	[[Category: Adman ET]]
-	[[Category: Sieker~~, L C~~]]	+	[[Category: Jensen LH]]
		+	[[Category: Sieker LC]]

OCA at 14:46, 5 August 2016

2016-08-05T14:46:48Z

←Older revision		Revision as of 14:46, 5 August 2016
Line 1:		Line 1:
		+
	==STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION==		==STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION==
	<StructureSection load='7rxn' size='340' side='right' caption='[[7rxn]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='7rxn' size='340' side='right' caption='[[7rxn]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris Desulfovibrio vulgaris~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7RXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7RXN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB], [http://www.ebi.ac.uk/pdbsum/7rxn 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=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [http://pdbe.org/7rxn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB], [http://www.ebi.ac.uk/pdbsum/7rxn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7rxn 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=7rxn 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 7rxn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio vulgaris~~]]	+	[[Category: Atcc 29579]]
	[[Category: Adman, E T]]		[[Category: Adman, E T]]
	[[Category: Jensen, L H]]		[[Category: Jensen, L H]]
	[[Category: Sieker, L C]]		[[Category: Sieker, L C]]

OCA at 19:41, 25 December 2014

2014-12-25T19:41:11Z

←Older revision		Revision as of 19:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7RXN FirstGlance]. <br>		<table><tr><td colspan='2'>[[7rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7RXN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB], [http://www.ebi.ac.uk/pdbsum/7rxn 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=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB], [http://www.ebi.ac.uk/pdbsum/7rxn PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RUBR_DESVH RUBR_DESVH]] Rubredoxin is a small nonheme, iron protein lacking acid-labile sulfide. Its single Fe, chelated to 4 Cys, functions as an electron acceptor and may also stabilize the conformation of the molecule. Electron acceptor for cytoplasmic lactate dehydrogenase.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
-	[[Category: Adman, E T.]]	+	[[Category: Adman, E T]]
-	[[Category: Jensen, L H.]]	+	[[Category: Jensen, L H]]
-	[[Category: Sieker, L C.]]	+	[[Category: Sieker, L C]]

OCA: Protected "7rxn" [edit=sysop:move=sysop]

2014-06-05T07:40:26Z

Protected "7rxn" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:40, 5 June 2014

OCA at 07:40, 5 June 2014

2014-06-05T07:40:24Z

←Older revision		Revision as of 07:40, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION==
-	[[~~Image~~:7rxn.~~png\|left~~\|200px]]	+	<StructureSection load='7rxn' size='340' side='right' caption='[[7rxn]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7RXN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB], [http://www.ebi.ac.uk/pdbsum/7rxn 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/rx/7rxn_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 X-ray model of rubredoxin from Desulfovibrio vulgaris has been refined against 1.5 A X-ray diffraction data collected on a diffractometer. The final model comprises 395 non-hydrogen protein atoms, and 180 solvent O atoms. The final R-value for the model with calculated H atom positions included as fixed contributions is 0.098 over all reflections greater than 2 sigma I from infinity to 1.5 A. The error in co-ordinates is estimated to be 0.08 A. The solvent model was twice redetermined during the later stages of refinement and was instrumental in its success. One sequence error has been detected and corrected (Thr21----Asp). The iron-sulfur site bond angles are distorted from true tetrahedral symmetry, as found in other rubredoxin structures. A significant deviation from tetrahedral angles is seen at C alpha atoms 9, 10, 42 and 43, interior angles of the loops binding the iron atom. The planes of two aromatic groups, Tyr4 and Trp37, are nearly parallel to, and lie under, an extended system of atoms that includes the peptide bonds preceding the first cysteine residue of each cysteine loop as well as the cysteine side-chain, the iron, and the cysteine side-chain of the opposite loop, forming a previously unrecognized extended system that may function in electron transfer.

-	~~<!--~~	+	Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution.,Adman ET, Sieker LC, Jensen LH J Mol Biol. 1991 Jan 20;217(2):337-52. PMID:1992166<ref>PMID:1992166</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_7rxn"~~, ~~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_7rxn\| PDB=7rxn \| SCENE= }}~~	+

-	~~===STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_1992166}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on~~ PubMed ~~at http://www.pubmed.gov)~~, ~~where 1992166 is the PubMed ID number.~~	+	</StructureSection>
-	~~-->~~	+
-	~~{{ABSTRACT_PUBMED_1992166}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~7RXN is~~ a ~~1 chain structure~~ of ~~sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:1992166<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Adman, E T.]]		[[Category: Adman, E T.]]
	[[Category: Jensen, L H.]]		[[Category: Jensen, L H.]]
	[[Category: Sieker, L C.]]		[[Category: Sieker, L C.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:51:48 2009''

OCA at 02:51, 18 February 2009

2009-02-18T02:51:50Z

←Older revision		Revision as of 02:51, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	7RXN is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].	+	7RXN is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].

	==Reference==		==Reference==
-	~~Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution., Adman ET, Sieker LC, Jensen LH, J Mol Biol. 1991 Jan 20;217(2):337-52.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/1992166 1992166]~~	+	<ref group="xtra">PMID:1992166</ref><references group="xtra"/>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
-	[[Category: Single protein]]
	[[Category: Adman, E T.]]		[[Category: Adman, E T.]]
	[[Category: Jensen, L H.]]		[[Category: Jensen, L H.]]
	[[Category: Sieker, L C.]]		[[Category: Sieker, L C.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 3 15~~:02:~~27 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:51:48 2009''

OCA at 12:02, 3 July 2008

2008-07-03T12:02:33Z

←Older revision		Revision as of 12:02, 3 July 2008
Line 1:		Line 1:
-	[[Image:7rxn.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:7rxn.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_7rxn\| PDB=7rxn \| SCENE= }}		{{STRUCTURE_7rxn\| PDB=7rxn \| SCENE= }}

-	~~'''~~STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION~~'''~~	+	===STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION===


-	~~==Overview==~~	+	<!--
-	~~The X~~-~~ray model of rubredoxin from Desulfovibrio vulgaris has been refined against 1.5 A X~~-~~ray diffraction data collected on a diffractometer.~~ The ~~final model comprises 395 non-hydrogen protein atoms~~, ~~and 180 solvent O atoms. The final R-value for~~ the ~~model with calculated H atom positions included~~ as ~~fixed contributions is 0~~.~~098 over all reflections greater than 2 sigma I from infinity to 1~~.5 A. The error in co-ordinates is estimated to be 0.08 A. The solvent model was twice redetermined during the later stages of refinement and was instrumental in its success. One sequence error has been detected and corrected (Thr21----Asp)~~. The iron-sulfur site bond angles are distorted from true tetrahedral symmetry~~, ~~as found in other rubredoxin structures. A significant deviation from tetrahedral angles~~ is ~~seen at C alpha atoms 9, 10, 42 and 43, interior angles of~~ the ~~loops binding the iron atom~~. The planes of two aromatic groups, Tyr4 and Trp37, are nearly parallel to, and lie under, an extended system of atoms that includes the peptide bonds preceding the first cysteine residue of each cysteine loop as well as the cysteine side-~~chain, the iron, and the cysteine side~~-~~chain of the opposite loop, forming a previously unrecognized extended system that may function in electron transfer.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_1992166}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 1992166 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_1992166}}

	==About this Structure==		==About this Structure==
Line 25:		Line 29:
	[[Category: Jensen, L H.]]		[[Category: Jensen, L H.]]
	[[Category: Sieker, L C.]]		[[Category: Sieker, L C.]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May~~ ~~4 22~~:47:43 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jul 3 15:02:27 2008''

OCA at 19:47, 4 May 2008

2008-05-04T19:47:44Z

←Older revision		Revision as of 19:47, 4 May 2008
Line 1:		Line 1:
	[[Image:7rxn.gif\|left\|200px]]		[[Image:7rxn.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 7rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>7rxn</scene>~~, ~~resolution 1~~.~~5Å~~	+	The line below this paragraph, containing "STRUCTURE_7rxn", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=FE:FE+(III~~)~~+ION'>FE</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY=~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE=~~	+	-->
-	\|~~DOMAIN~~=	+	{{STRUCTURE_7rxn\| PDB=7rxn \| SCENE= }}
-	\|~~RELATEDENTRY~~=	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [http://www.ebi.ac.uk/pdbsum/7rxn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB]</span>	+
-	}}	+

	'''STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION'''		'''STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION'''
Line 19:		Line 16:

	==About this Structure==		==About this Structure==
-	7RXN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry ~~3RXN~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].	+	7RXN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rxn 3rxn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].

	==Reference==		==Reference==
Line 28:		Line 25:
	[[Category: Jensen, L H.]]		[[Category: Jensen, L H.]]
	[[Category: Sieker, L C.]]		[[Category: Sieker, L C.]]
-	~~[[Category: electron transfer(iron-sulfur protein)]]~~	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:47:43 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:44:45 2008''	+

OCA at 02:44, 31 March 2008

2008-03-31T02:44:48Z

←Older revision		Revision as of 02:44, 31 March 2008
Line 4:		Line 4:
	\|PDB= 7rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>7rxn</scene>, resolution 1.5Å		\|PDB= 7rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>7rxn</scene>, resolution 1.5Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> ~~and~~ <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>	+	\|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
	\|ACTIVITY=		\|ACTIVITY=
	\|GENE=		\|GENE=
		+	\|DOMAIN=
		+	\|RELATEDENTRY=
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=7rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rxn OCA], [http://www.ebi.ac.uk/pdbsum/7rxn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=7rxn RCSB]</span>
	}}		}}

Line 25:		Line 28:
	[[Category: Jensen, L H.]]		[[Category: Jensen, L H.]]
	[[Category: Sieker, L C.]]		[[Category: Sieker, L C.]]
-	[[Category: FE]]
-	[[Category: SO4]]
	[[Category: electron transfer(iron-sulfur protein)]]		[[Category: electron transfer(iron-sulfur protein)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:15:05 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:44:45 2008''

OCA at 17:15, 20 March 2008

2008-03-20T17:15:06Z

←Older revision		Revision as of 17:15, 20 March 2008
Line 1:		Line 1:
-	[[Image:7rxn.gif\|left\|200px]]~~<br /><applet load~~="7rxn~~" size~~="350~~" color~~=~~"white" frame="true" align="right" spinBox~~=~~"true"~~	+	[[Image:7rxn.gif\|left\|200px]]
-	~~caption="~~7rxn, resolution 1.5Å" />	+
-	'''STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION'''~~<br />~~	+	{{Structure
		+	\|PDB= 7rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>7rxn</scene>, resolution 1.5Å
		+	\|SITE=
		+	\|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
		+	\|ACTIVITY=
		+	\|GENE=
		+	}}
		+
		+	'''STRUCTURE OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.5 A RESOLUTION'''
		+

	==Overview==		==Overview==
Line 7:		Line 16:

	==About this Structure==		==About this Structure==
-	7RXN is a [~~http://en.wikipedia.org/wiki/Single_protein~~ Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris~~] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligands ligands~~]. This structure supersedes the now removed PDB entry 3RXN. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].	+	7RXN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. This structure supersedes the now removed PDB entry 3RXN. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RXN OCA].

	==Reference==		==Reference==
-	Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution., Adman ET, Sieker LC, Jensen LH, J Mol Biol. 1991 Jan 20;217(2):337-52. PMID:[http://~~ispc~~.~~weizmann~~.ac.~~il/~~/~~pmbin~~/~~getpm?pmid=~~1992166 1992166]	+	Structure of rubredoxin from Desulfovibrio vulgaris at 1.5 A resolution., Adman ET, Sieker LC, Jensen LH, J Mol Biol. 1991 Jan 20;217(2):337-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1992166 1992166]
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Single protein]]		[[Category: Single protein]]
Line 20:		Line 29:
	[[Category: electron transfer(iron-sulfur protein)]]		[[Category: electron transfer(iron-sulfur protein)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Feb 21~~ 19:17:33 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:15:05 2008''