8rxn - Revision history

OCA at 09:43, 14 February 2024

OCA — Wed, 14 Feb 2024 09:43:49 GMT

←Older revision		Revision as of 09:43, 14 February 2024
Line 1:		Line 1:
		+
	==REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS==		==REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS==
-	<StructureSection load='8rxn' size='340' side='right' caption='[[8rxn]], [[Resolution\|resolution]] 1.00Å' scene=''>	+	<StructureSection load='8rxn' size='340' side='right'caption='[[8rxn]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_29579 Atcc 29579~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=8RXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8RXN 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]] 1Å</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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [~~http~~://pdbe.org/8rxn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/8rxn PDBsum]</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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [https://pdbe.org/8rxn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [https://www.ebi.ac.uk/pdbsum/8rxn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8rxn 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/8rxn_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/8rxn_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 18:		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=8rxn 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=8rxn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2(1) with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18,532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model.
-
-	Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints.,Dauter Z, Sieker LC, Wilson KS Acta Crystallogr B. 1992 Feb 1;48 ( Pt 1):42-59. PMID:1616692<ref>PMID:1616692</ref>

-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+	==See Also==
-	~~</div>~~	+	*[[Rubredoxin 3D structures\|Rubredoxin 3D structures]]
-	~~<div class~~=~~"pdbe-citations 8rxn" style~~=~~"background-color:#fffaf0;"></div>~~	+	*[[Rubredoxin PDB structures\|Rubredoxin PDB structures]]
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 29579~~]]	+	[[Category: Desulfovibrio vulgaris]]
-	[[Category: Dauter, Z]]	+	[[Category: Large Structures]]
-	[[Category: Sieker, L]]	+	[[Category: Dauter Z]]
-	[[Category: Wilson, K]]	+	[[Category: Sieker L]]
		+	[[Category: Wilson K]]

OCA at 17:16, 9 February 2016

OCA — Tue, 09 Feb 2016 17:16:29 GMT

←Older revision		Revision as of 17:16, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='8rxn' size='340' side='right' caption='[[8rxn]], [[Resolution\|resolution]] 1.00Å' scene=''>		<StructureSection load='8rxn' size='340' side='right' caption='[[8rxn]], [[Resolution\|resolution]] 1.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris Desulfovibrio vulgaris~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8RXN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8RXN 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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [http://www.ebi.ac.uk/pdbsum/8rxn 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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [http://pdbe.org/8rxn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [http://www.ebi.ac.uk/pdbsum/8rxn PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	<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=8rxn ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 8rxn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio vulgaris~~]]	+	[[Category: Atcc 29579]]
	[[Category: Dauter, Z]]		[[Category: Dauter, Z]]
	[[Category: Sieker, L]]		[[Category: Sieker, L]]
	[[Category: Wilson, K]]		[[Category: Wilson, K]]

OCA at 08:18, 25 December 2014

OCA — Thu, 25 Dec 2014 08:18:50 GMT

←Older revision		Revision as of 08:18, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8RXN FirstGlance]. <br>		<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8RXN 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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [http://www.ebi.ac.uk/pdbsum/8rxn 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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [http://www.ebi.ac.uk/pdbsum/8rxn 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: Dauter, Z.]]	+	[[Category: Dauter, Z]]
-	[[Category: Sieker, L.]]	+	[[Category: Sieker, L]]
-	[[Category: Wilson, K.]]	+	[[Category: Wilson, K]]

OCA: Protected "8rxn" [edit=sysop:move=sysop]

OCA — Thu, 05 Jun 2014 09:18:25 GMT

Protected "8rxn" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:18, 5 June 2014

OCA at 09:18, 5 June 2014

OCA — Thu, 05 Jun 2014 09:18:24 GMT

←Older revision		Revision as of 09:18, 5 June 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS==
-	[[~~Image~~:8rxn.~~png\|left~~\|200px]]	+	<StructureSection load='8rxn' size='340' side='right' caption='[[8rxn]], [[Resolution\|resolution]] 1.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8rxn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8RXN 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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB], [http://www.ebi.ac.uk/pdbsum/8rxn 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/8rxn_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 ==
		+	X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2(1) with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18,532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model.

-	~~<!--~~	+	Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints.,Dauter Z, Sieker LC, Wilson KS Acta Crystallogr B. 1992 Feb 1;48 ( Pt 1):42-59. PMID:1616692<ref>PMID:1616692</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_8rxn"~~, ~~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_8rxn\| PDB=8rxn \| SCENE= }}~~	+

-	~~===REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_1616692}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 1616692 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_1616692}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~8RXN is a 1 chain structure of sequence from [http:~~/~~/en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:1616692<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Dauter, Z.]]		[[Category: Dauter, Z.]]
	[[Category: Sieker, L.]]		[[Category: Sieker, L.]]
	[[Category: Wilson, K.]]		[[Category: Wilson, K.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:27:24 2009''

OCA at 09:27, 17 February 2009

OCA — Tue, 17 Feb 2009 09:27:25 GMT

←Older revision		Revision as of 09:27, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	8RXN is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].	+	8RXN is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].

	==Reference==		==Reference==
-	~~Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints., Dauter Z, Sieker LC, Wilson KS, Acta Crystallogr B. 1992 Feb 1;48 ( Pt 1):42-59.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/1616692 1616692]~~	+	<ref group="xtra">PMID:1616692</ref><references group="xtra"/>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
-	[[Category: Single protein]]
	[[Category: Dauter, Z.]]		[[Category: Dauter, Z.]]
	[[Category: Sieker, L.]]		[[Category: Sieker, L.]]
	[[Category: Wilson, K.]]		[[Category: Wilson, K.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Fri Jul~~ 11 12:54:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:27:24 2009''

OCA at 09:54, 11 July 2008

OCA — Fri, 11 Jul 2008 09:54:21 GMT

←Older revision		Revision as of 09:54, 11 July 2008
Line 1:		Line 1:
-	[[Image:8rxn.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:8rxn.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_8rxn\| PDB=8rxn \| SCENE= }}		{{STRUCTURE_8rxn\| PDB=8rxn \| SCENE= }}

-	~~'''~~REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS~~'''~~	+	===REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS===


-	~~==Overview==~~	+	<!--
-	X-~~ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X~~-~~rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector.~~ The ~~space group of the crystals is P2(1) with cell dimensions a = 19.97~~, ~~b = 41.45~~, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to ~~an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in~~ the ~~refinement~~. ~~There were 18,532 independent X-ray observations for a total of 1916 atomic parameters~~. ~~A round of unrestrained refinement gave an R factor of 16.0%~~, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the ~~present model~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_1616692}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 1616692 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_1616692}}

	==About this Structure==		==About this Structure==
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	[[Category: Sieker, L.]]		[[Category: Sieker, L.]]
	[[Category: Wilson, K.]]		[[Category: Wilson, K.]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 22~~:51:57 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Jul 11 12:54:20 2008''

OCA at 19:51, 4 May 2008

OCA — Sun, 04 May 2008 19:51:58 GMT

←Older revision		Revision as of 19:51, 4 May 2008
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	[[Image:8rxn.jpg\|left\|200px]]		[[Image:8rxn.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 8rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>8rxn</scene>~~, ~~resolution 1~~.~~0Å~~	+	The line below this paragraph, containing "STRUCTURE_8rxn", 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_8rxn\| PDB=8rxn \| SCENE= }}
-	\|~~RELATEDENTRY~~=	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [http://www.ebi.ac.uk/pdbsum/8rxn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB]</span>	+
-	}}	+

	'''REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS'''		'''REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS'''
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	[[Category: Sieker, L.]]		[[Category: Sieker, L.]]
	[[Category: Wilson, K.]]		[[Category: Wilson, K.]]
-	~~[[Category: electron transport(iron)]]~~	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 22:51:57 2008''
-		+
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31 05~~:45:46 2008''	+

OCA at 02:45, 31 March 2008

OCA — Mon, 31 Mar 2008 02:45:50 GMT

←Older revision		Revision as of 02:45, 31 March 2008
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	\|PDB= 8rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>8rxn</scene>, resolution 1.0Å		\|PDB= 8rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>8rxn</scene>, resolution 1.0Å
	\|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=8rxn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8rxn OCA], [http://www.ebi.ac.uk/pdbsum/8rxn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=8rxn RCSB]</span>
	}}		}}

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	[[Category: Sieker, L.]]		[[Category: Sieker, L.]]
	[[Category: Wilson, K.]]		[[Category: Wilson, K.]]
-	[[Category: FE]]
-	[[Category: SO4]]
	[[Category: electron transport(iron)]]		[[Category: electron transport(iron)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 19~~:16:03 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:45:46 2008''

OCA at 17:16, 20 March 2008

OCA — Thu, 20 Mar 2008 17:16:04 GMT

←Older revision		Revision as of 17:16, 20 March 2008
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-	[[Image:8rxn.jpg\|left\|200px]]~~<br /><applet load~~="8rxn~~" size~~="350~~" color~~=~~"white" frame~~=~~"true" align="right" spinBox="true"~~	+	[[Image:8rxn.jpg\|left\|200px]]
-	~~caption="~~8rxn, resolution 1.0Å" />	+
-	'''REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS'''~~<br />~~	+	{{Structure
		+	\|PDB= 8rxn \|SIZE=350\|CAPTION= <scene name='initialview01'>8rxn</scene>, resolution 1.0Å
		+	\|SITE=
		+	\|LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
		+	\|ACTIVITY=
		+	\|GENE=
		+	}}
		+
		+	'''REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS'''
		+

	==Overview==		==Overview==
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	==About this Structure==		==About this Structure==
-	8RXN 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~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].	+	8RXN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8RXN OCA].

	==Reference==		==Reference==
-	Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints., Dauter Z, Sieker LC, Wilson KS, Acta Crystallogr B. 1992 Feb 1;48 ( Pt 1):42-59. PMID:[http://~~ispc~~.~~weizmann~~.ac.~~il/~~/~~pmbin~~/~~getpm?pmid=~~1616692 1616692]	+	Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints., Dauter Z, Sieker LC, Wilson KS, Acta Crystallogr B. 1992 Feb 1;48 ( Pt 1):42-59. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1616692 1616692]
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Single protein]]		[[Category: Single protein]]
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	[[Category: electron transport(iron)]]		[[Category: electron transport(iron)]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu ~~Feb 21~~ 19:18:18 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:16:03 2008''