2kkd - Revision history

OCA at 09:39, 22 May 2024

OCA — Wed, 22 May 2024 09:39:46 GMT

←Older revision		Revision as of 09:39, 22 May 2024
Line 1:		Line 1:

	==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==		==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==
-	<StructureSection load='2kkd' size='340' side='right'caption='[[2kkd~~]], [[NMR_Ensembles_of_Models \| 15 NMR models~~]]' scene=''>	+	<StructureSection load='2kkd' size='340' side='right'caption='[[2kkd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Desvh Desvh~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._Hildenborough Desulfovibrio vulgaris str. Hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KKD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style~~=~~'overflow: auto; max-height: 3em;'~~>~~[[8rxn\|8rxn]], [[2ql0\|2ql0]]~~<~~/div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">rub, DVU_3184 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])~~</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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [https://pdbe.org/2kkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [https://www.ebi.ac.uk/pdbsum/2kkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kkd 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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [https://pdbe.org/2kkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [https://www.ebi.ac.uk/pdbsum/2kkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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.	+	[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]]
Line 30:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2kkd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2kkd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rubredoxin 3D structures\|Rubredoxin 3D structures]]
		+	*[[Rubredoxin PDB structures\|Rubredoxin PDB structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desvh~~]]	+	[[Category: Desulfovibrio vulgaris str. Hildenborough]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Duarte~~, I C~~]]	+	[[Category: Duarte IC]]
-	[[Category: Macedo~~, A L~~]]	+	[[Category: Macedo AL]]
-	[[Category: Markley~~, J L~~]]	+	[[Category: Markley JL]]
-	[[Category: Moura, I]]	+	[[Category: Moura I]]
-	[[Category: Moura~~, J J.G~~]]	+	[[Category: Moura JJG]]
-	[[Category: Nunes~~, S G~~]]	+	[[Category: Nunes SG]]
-	[[Category: Volkman~~, B F]]~~	+	[[Category: Volkman BF]]
-	~~[[Category: Cytoplasm]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 07:27, 14 April 2021

OCA — Wed, 14 Apr 2021 07:27:24 GMT

←Older revision		Revision as of 07:27, 14 April 2021
Line 1:		Line 1:

	==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==		==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==
-	<StructureSection load='2kkd' size='340' side='right' caption='[[2kkd]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>	+	<StructureSection load='2kkd' size='340' side='right'caption='[[2kkd]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Desvh Desvh]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2KKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desvh Desvh]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KKD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[8rxn\|8rxn]], [[2ql0\|2ql0]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [~~http~~://pdbe.org/2kkd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2kkd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2kkd 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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [https://pdbe.org/2kkd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [https://www.ebi.ac.uk/pdbsum/2kkd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kkd 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]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Desvh]]		[[Category: Desvh]]
		+	[[Category: Large Structures]]
	[[Category: Duarte, I C]]		[[Category: Duarte, I C]]
	[[Category: Macedo, A L]]		[[Category: Macedo, A L]]

OCA at 11:17, 18 July 2018

OCA — Wed, 18 Jul 2018 11:17:39 GMT

←Older revision		Revision as of 11:17, 18 July 2018
Line 1:		Line 1:
		+
	==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==		==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==
	<StructureSection load='2kkd' size='340' side='right' caption='[[2kkd]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>		<StructureSection load='2kkd' size='340' side='right' caption='[[2kkd]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://pdbe.org/2kkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd 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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://pdbe.org/2kkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2kkd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kk/2kkd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kk/2kkd_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 41:		Line 42:
	[[Category: Nunes, S G]]		[[Category: Nunes, S G]]
	[[Category: Volkman, B F]]		[[Category: Volkman, B F]]
		+	[[Category: Cytoplasm]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Transport]]		[[Category: Transport]]

OCA at 03:38, 7 February 2016

OCA — Sun, 07 Feb 2016 03:38:53 GMT

←Older revision		Revision as of 03:38, 7 February 2016
Line 18:		Line 18:
	<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=2kkd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:24, 9 September 2015

OCA — Wed, 09 Sep 2015 21:24:25 GMT

←Older revision		Revision as of 21:24, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='2kkd' size='340' side='right' caption='[[2kkd]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>		<StructureSection load='2kkd' size='340' side='right' caption='[[2kkd]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KKD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desvh Desvh]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KKD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 ~~Desulfovibrio vulgaris str. Hildenborough~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 DESVH])</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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd 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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://pdbe.org/2kkd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2kkd" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio vulgaris str. hildenborough~~]]	+	[[Category: Desvh]]
	[[Category: Duarte, I C]]		[[Category: Duarte, I C]]
	[[Category: Macedo, A L]]		[[Category: Macedo, A L]]

OCA at 07:34, 24 December 2014

OCA — Wed, 24 Dec 2014 07:34:57 GMT

←Older revision		Revision as of 07:34, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KKD FirstGlance]. <br>		<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KKD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 Desulfovibrio vulgaris str. Hildenborough])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 Desulfovibrio vulgaris str. Hildenborough])</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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd 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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd 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 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio vulgaris str. hildenborough]]		[[Category: Desulfovibrio vulgaris str. hildenborough]]
-	[[Category: Duarte, I C.]]	+	[[Category: Duarte, I C]]
-	[[Category: Macedo, A L.]]	+	[[Category: Macedo, A L]]
-	[[Category: Markley, J L.]]	+	[[Category: Markley, J L]]
-	[[Category: Moura, I.]]	+	[[Category: Moura, I]]
-	[[Category: Moura, J J.G.]]	+	[[Category: Moura, J J.G]]
-	[[Category: Nunes, S G.]]	+	[[Category: Nunes, S G]]
-	[[Category: Volkman, B F.]]	+	[[Category: Volkman, B F]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Transport]]		[[Category: Transport]]

OCA at 08:19, 30 September 2014

OCA — Tue, 30 Sep 2014 08:19:14 GMT

←Older revision		Revision as of 08:19, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2kkd.~~png~~\|~~left~~\|200px]]	+	==NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin==
		+	<StructureSection load='2kkd' size='340' side='right' caption='[[2kkd]], [[NMR_Ensembles_of_Models \| 15 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2KKD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[8rxn\|8rxn]], [[2ql0\|2ql0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rub, DVU_3184 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=882 Desulfovibrio vulgaris str. Hildenborough])</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=2kkd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kkd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2kkd RCSB], [http://www.ebi.ac.uk/pdbsum/2kkd 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/kk/2kkd_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 Ni(II) and Zn(II) derivatives of Desulfovibrio vulgaris rubredoxin (DvRd) have been studied by NMR spectroscopy to probe the structure at the metal centre. The betaCH(2) proton pairs from the cysteines that bind the Ni(II) atom have been identified using 1D nuclear Overhauser enhancement (NOE) difference spectra and sequence specifically assigned via NOE correlations to neighbouring protons and by comparison with the published X-ray crystal structure of a Ni(II) derivative of Clostridium pasteurianum rubredoxin. The solution structures of DvRd(Zn) and DvRd(Ni) have been determined and the paramagnetic form refined using pseudocontact shifts. The determination of the magnetic susceptibility anisotropy tensor allowed the contact and pseudocontact contributions to the observed chemical shifts to be obtained. Analysis of the pseudocontact and contact chemical shifts of the cysteine Hbeta protons and backbone protons close to the metal centre allowed conclusions to be drawn as to the geometry and hydrogen-bonding pattern at the metal binding site. The importance of NH-S hydrogen bonds at the metal centre for the delocalization of electron spin density is confirmed for rubredoxins and can be extrapolated to metal centres in Cu proteins: amicyanin, plastocyanin, stellacyanin, azurin and pseudoazurin.

-	~~{{STRUCTURE_2kkd\| PDB=2kkd \| SCENE= }}~~	+	An NMR structural study of nickel-substituted rubredoxin.,Goodfellow BJ, Duarte IC, Macedo AL, Volkman BF, Nunes SG, Moura I, Markley JL, Moura JJ J Biol Inorg Chem. 2009 Dec 8. PMID:19997764<ref>PMID:19997764</ref>

-	~~===NMR Structure~~ of ~~Ni Substitued Desulfovibrio vulgaris Rubredoxin===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19997764}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019997764<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Desulfovibrio vulgaris str. hildenborough]]		[[Category: Desulfovibrio vulgaris str. hildenborough]]
	[[Category: Duarte, I C.]]		[[Category: Duarte, I C.]]

OCA: Protected "2kkd" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 10:45:24 GMT

Protected "2kkd" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:45, 7 January 2013

OCA at 10:45, 7 January 2013

OCA — Mon, 07 Jan 2013 10:45:22 GMT

←Older revision		Revision as of 10:45, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2kkd.png\|left\|200px]]		[[Image:2kkd.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2kkd", 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_2kkd\| PDB=2kkd \| SCENE= }}		{{STRUCTURE_2kkd\| PDB=2kkd \| SCENE= }}

	===NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin===		===NMR Structure of Ni Substitued Desulfovibrio vulgaris Rubredoxin===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19997764}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19997764 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19997764}}		{{ABSTRACT_PUBMED_19997764}}

	==About this Structure==		==About this Structure==
-	~~2KKD~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA].	+	[[2kkd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19997764~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019997764</ref><references group="xtra"/>
	[[Category: Desulfovibrio vulgaris str. hildenborough]]		[[Category: Desulfovibrio vulgaris str. hildenborough]]
	[[Category: Duarte, I C.]]		[[Category: Duarte, I C.]]
Line 32:		Line 20:
	[[Category: Nunes, S G.]]		[[Category: Nunes, S G.]]
	[[Category: Volkman, B F.]]		[[Category: Volkman, B F.]]
-	[[Category: Cytoplasm]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Transport]]		[[Category: Transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 27 19:27:58 2010''

OCA at 17:27, 27 January 2010

OCA — Wed, 27 Jan 2010 17:27:58 GMT

←Older revision		Revision as of 17:27, 27 January 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:2kkd.~~jpg~~\|left\|200px]]	+	[[Image:2kkd.png\|left\|200px]]

	<!--		<!--
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2KKD is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA].	+	2KKD is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris_str._hildenborough Desulfovibrio vulgaris str. hildenborough]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2qkz 2qkz]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KKD OCA].

	==Reference==		==Reference==
Line 38:		Line 38:
	[[Category: Transport]]		[[Category: Transport]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Dec 24 07~~:36:~~15 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 27 19:27:58 2010''