1kwj - Revision history

OCA at 08:04, 3 April 2024

OCA — Wed, 03 Apr 2024 08:04:21 GMT

←Older revision		Revision as of 08:04, 3 April 2024
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	==solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure==		==solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure==
-	<StructureSection load='1kwj' size='340' side='right'caption='[[1kwj~~]], [[NMR_Ensembles_of_Models \| 1 NMR models~~]]' scene=''>	+	<StructureSection load='1kwj' size='340' side='right'caption='[[1kwj]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Chloropseudomonas_ethylica Chloropseudomonas ethylica~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfuromonas_acetoxidans Desulfuromonas acetoxidans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEC:HEME+C'>HEC</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;~~'>~~[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [https://pdbe.org/1kwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [https://www.ebi.ac.uk/pdbsum/1kwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwj 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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [https://pdbe.org/1kwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [https://www.ebi.ac.uk/pdbsum/1kwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CYC3_DESAC CYC3_DESAC]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.	+	[https://www.uniprot.org/uniprot/CYC3_DESAC CYC3_DESAC] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1kwj 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=1kwj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Lysines 9 and 10 in Desulfuromonas acetoxidans cytochrome c7, which could be involved in the interaction mechanism with the redox partners, have been replaced by alanine residues using site-directed mutagenesis. The solution structure of the fully oxidized form of K9-10A cytochrome c7, which is paramagnetic with three paramagnetic centers, has been determined via 1H NMR. The assignment of the spectra has been performed through an automatic program whose algorithm and strategy are here described. The assignment of the NOESY spectra has been further extended by back calculating the NOESY maps. The final number of meaningful NOE-based upper distance limits was 1186. In the Restrained Energy Minimization calculations, 147 pseudocontact shift constraints were also included, which showed consistency with NOE-based constraints and therefore further contribute to validate the structure quality. A final family of 35 conformers was calculated with RMSD values with respect to the mean structure of 0.69 +/- 0.17 A and 1.05 +/- 0.14 A for the backbone and heavy atoms, respectively. The overall fold of the molecule is maintained with respect to the native protein. The loop present between heme III and heme IV results to be highly disordered also in the present structure although its overall shape mainly resembles that of the oxidized native protein, and the two strands which give rise to the short beta-sheet present at the N-terminus and connected by a turn containing the mutated residues, are less clearly defined. If this loop is neglected, the RMSD values are 0.52 +/- 0.07 A and 0.92 +/- 0.06 A for the backbone and heavy atoms, respectively, which represent a reasonable resolution. The relative distances and orientations of the three hemes are maintained, as well as the orientation of the imidazole rings of the axial histidine ligands, with the only exception of heme IV. Such difference probably reflects minor conformational changes due to the substitution of the vicinal Lys 10 with an Ala. The replacement of the two lysines does not affect the reduction potentials of the three hemes, consistently with the expectations on the basis of the structure and electrostatic calculations. However, the replacement of the two lysines affects the reactivity of the mutant cytochrome c7 with [Fe] hydrogenase, inducing a change in Km. This finding is in agreement with the identification of the protein area around heme IV as the interacting site.
-
-	A quick solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans and mechanistic implications.,Assfalg M, Bertini I, Turano P, Bruschi M, Durand MC, Giudici-Orticoni MT, Dolla A J Biomol NMR. 2002 Feb;22(2):107-22. PMID:11883773<ref>PMID:11883773</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1kwj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]		*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chloropseudomonas ethylica~~]]	+	[[Category: Desulfuromonas acetoxidans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Assfalg, M]]	+	[[Category: Assfalg M]]
-	[[Category: Bertini, I]]	+	[[Category: Bertini I]]
-	[[Category: Bruschi, M]]	+	[[Category: Bruschi M]]
-	[[Category: Dolla, A]]	+	[[Category: Dolla A]]
-	[[Category: Durand~~, M C~~]]	+	[[Category: Durand MC]]
-	[[Category: Giudici-Orticoni~~, M T~~]]	+	[[Category: Giudici-Orticoni MT]]
-	[[Category: Turano, P]]	+	[[Category: Turano P]]
-	~~[[Category: Automatic assignment]]~~	+
-	~~[[Category: Cytochrome c7]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Multiheme cytochrome]]~~	+
-	~~[[Category: Nmr solution structure]]~~	+
-	~~[[Category: Oxygen storage-transport complex~~]]	+

OCA at 06:36, 18 August 2021

OCA — Wed, 18 Aug 2021 06:36:32 GMT

←Older revision		Revision as of 06:36, 18 August 2021
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	<StructureSection load='1kwj' size='340' side='right'caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1kwj' size='340' side='right'caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Chloropseudomonas_ethylica Chloropseudomonas ethylica]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chloropseudomonas_ethylica Chloropseudomonas ethylica]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</div></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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [~~http~~://pdbe.org/1kwj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1kwj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwj 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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [https://pdbe.org/1kwj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [https://www.ebi.ac.uk/pdbsum/1kwj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CYC3_DESAC CYC3_DESAC]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.	+	[[https://www.uniprot.org/uniprot/CYC3_DESAC CYC3_DESAC]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:02, 13 November 2019

OCA — Wed, 13 Nov 2019 12:02:28 GMT

←Older revision		Revision as of 12:02, 13 November 2019
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	==solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure==		==solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure==
-	<StructureSection load='1kwj' size='340' side='right' caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>	+	<StructureSection load='1kwj' size='340' side='right'caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chloropseudomonas_ethylica Chloropseudomonas ethylica]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chloropseudomonas_ethylica Chloropseudomonas ethylica]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1kwj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kwj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Chloropseudomonas ethylica]]		[[Category: Chloropseudomonas ethylica]]
		+	[[Category: Large Structures]]
	[[Category: Assfalg, M]]		[[Category: Assfalg, M]]
	[[Category: Bertini, I]]		[[Category: Bertini, I]]

OCA at 21:12, 24 January 2018

OCA — Wed, 24 Jan 2018 21:12:47 GMT

←Older revision		Revision as of 21:12, 24 January 2018
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		+
	==solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure==		==solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure==
	<StructureSection load='1kwj' size='340' side='right' caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1kwj' size='340' side='right' caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [http://pdbe.org/1kwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [http://www.ebi.ac.uk/pdbsum/1kwj 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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [http://pdbe.org/1kwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [http://www.ebi.ac.uk/pdbsum/1kwj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1kwj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kwj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kw/1kwj_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 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1kwj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1kwj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome c\|Cytochrome c]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:50, 8 February 2016

OCA — Mon, 08 Feb 2016 08:50:53 GMT

←Older revision		Revision as of 08:50, 8 February 2016
Line 17:		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=1kwj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:54, 10 September 2015

OCA — Thu, 10 Sep 2015 09:54:35 GMT

←Older revision		Revision as of 09:54, 10 September 2015
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	<StructureSection load='1kwj' size='340' side='right' caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>		<StructureSection load='1kwj' size='340' side='right' caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfuromonas_acetoxidans Desulfuromonas acetoxidans~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Chloropseudomonas_ethylica Chloropseudomonas ethylica]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [http://www.ebi.ac.uk/pdbsum/1kwj 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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [http://pdbe.org/1kwj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [http://www.ebi.ac.uk/pdbsum/1kwj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1kwj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfuromonas acetoxidans~~]]	+	[[Category: Chloropseudomonas ethylica]]
	[[Category: Assfalg, M]]		[[Category: Assfalg, M]]
	[[Category: Bertini, I]]		[[Category: Bertini, I]]

OCA at 22:05, 24 December 2014

OCA — Wed, 24 Dec 2014 22:05:00 GMT

←Older revision		Revision as of 22:05, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfuromonas_acetoxidans Desulfuromonas acetoxidans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfuromonas_acetoxidans Desulfuromonas acetoxidans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [http://www.ebi.ac.uk/pdbsum/1kwj 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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [http://www.ebi.ac.uk/pdbsum/1kwj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYC3_DESAC CYC3_DESAC]] Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Desulfuromonas acetoxidans]]		[[Category: Desulfuromonas acetoxidans]]
-	[[Category: Assfalg, M.]]	+	[[Category: Assfalg, M]]
-	[[Category: Bertini, I.]]	+	[[Category: Bertini, I]]
-	[[Category: Bruschi, M.]]	+	[[Category: Bruschi, M]]
-	[[Category: Dolla, A.]]	+	[[Category: Dolla, A]]
-	[[Category: Durand, M C.]]	+	[[Category: Durand, M C]]
-	[[Category: Giudici-Orticoni, M T.]]	+	[[Category: Giudici-Orticoni, M T]]
-	[[Category: Turano, P.]]	+	[[Category: Turano, P]]
	[[Category: Automatic assignment]]		[[Category: Automatic assignment]]
	[[Category: Cytochrome c7]]		[[Category: Cytochrome c7]]

OCA at 13:04, 28 September 2014

OCA — Sun, 28 Sep 2014 13:04:18 GMT

←Older revision		Revision as of 13:04, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1kwj.~~png~~\|~~left~~\|200px]]	+	==solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure==
		+	<StructureSection load='1kwj' size='340' side='right' caption='[[1kwj]], [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfuromonas_acetoxidans Desulfuromonas acetoxidans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KWJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ehj\|1ehj]], [[1f22\|1f22]], [[1new\|1new]], [[2new\|2new]], [[1hh5\|1hh5]], [[1l3o\|1l3o]]</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=1kwj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kwj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kwj RCSB], [http://www.ebi.ac.uk/pdbsum/1kwj 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/kw/1kwj_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 ==
		+	Lysines 9 and 10 in Desulfuromonas acetoxidans cytochrome c7, which could be involved in the interaction mechanism with the redox partners, have been replaced by alanine residues using site-directed mutagenesis. The solution structure of the fully oxidized form of K9-10A cytochrome c7, which is paramagnetic with three paramagnetic centers, has been determined via 1H NMR. The assignment of the spectra has been performed through an automatic program whose algorithm and strategy are here described. The assignment of the NOESY spectra has been further extended by back calculating the NOESY maps. The final number of meaningful NOE-based upper distance limits was 1186. In the Restrained Energy Minimization calculations, 147 pseudocontact shift constraints were also included, which showed consistency with NOE-based constraints and therefore further contribute to validate the structure quality. A final family of 35 conformers was calculated with RMSD values with respect to the mean structure of 0.69 +/- 0.17 A and 1.05 +/- 0.14 A for the backbone and heavy atoms, respectively. The overall fold of the molecule is maintained with respect to the native protein. The loop present between heme III and heme IV results to be highly disordered also in the present structure although its overall shape mainly resembles that of the oxidized native protein, and the two strands which give rise to the short beta-sheet present at the N-terminus and connected by a turn containing the mutated residues, are less clearly defined. If this loop is neglected, the RMSD values are 0.52 +/- 0.07 A and 0.92 +/- 0.06 A for the backbone and heavy atoms, respectively, which represent a reasonable resolution. The relative distances and orientations of the three hemes are maintained, as well as the orientation of the imidazole rings of the axial histidine ligands, with the only exception of heme IV. Such difference probably reflects minor conformational changes due to the substitution of the vicinal Lys 10 with an Ala. The replacement of the two lysines does not affect the reduction potentials of the three hemes, consistently with the expectations on the basis of the structure and electrostatic calculations. However, the replacement of the two lysines affects the reactivity of the mutant cytochrome c7 with [Fe] hydrogenase, inducing a change in Km. This finding is in agreement with the identification of the protein area around heme IV as the interacting site.

-	~~{{STRUCTURE_1kwj\| PDB=1kwj \| SCENE= }}~~	+	A quick solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans and mechanistic implications.,Assfalg M, Bertini I, Turano P, Bruschi M, Durand MC, Giudici-Orticoni MT, Dolla A J Biomol NMR. 2002 Feb;22(2):107-22. PMID:11883773<ref>PMID:11883773</ref>

-	~~===solution structure determination~~ of the ~~fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans, minimized average structure===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11883773}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1kwj]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfuromonas_acetoxidans Desulfuromonas acetoxidans]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c\|Cytochrome c]]		*[[Cytochrome c\|Cytochrome c]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011883773<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Desulfuromonas acetoxidans]]		[[Category: Desulfuromonas acetoxidans]]
	[[Category: Assfalg, M.]]		[[Category: Assfalg, M.]]

OCA at 09:36, 20 October 2012

OCA — Sat, 20 Oct 2012 09:36:11 GMT

←Older revision		Revision as of 09:36, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1kwj]] is a 1 chain structure ~~of [[Cytochrome c]]~~ with sequence from [http://en.wikipedia.org/wiki/Desulfuromonas_acetoxidans Desulfuromonas acetoxidans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA].	+	[[1kwj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfuromonas_acetoxidans Desulfuromonas acetoxidans]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KWJ OCA].

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

OCA: Protected "1kwj" [edit=sysop:move=sysop]

OCA — Wed, 25 Jul 2012 23:24:26 GMT

Protected "1kwj" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:24, 25 July 2012