2bq4 - Revision history

OCA at 11:23, 22 May 2024

OCA — Wed, 22 May 2024 11:23:06 GMT

←Older revision		Revision as of 11:23, 22 May 2024
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	<StructureSection load='2bq4' size='340' side='right'caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='2bq4' size='340' side='right'caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Desulfovibrio_africanus Desulfovibrio~~ africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfocurvibacter_africanus Desulfocurvibacter africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<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">X-ray diffraction, [[Resolution\|Resolution]] 1.68Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1a2i\|1a2i]]~~, [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [https://pdbe.org/2bq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [https://www.ebi.ac.uk/pdbsum/2bq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bq4 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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [https://pdbe.org/2bq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [https://www.ebi.ac.uk/pdbsum/2bq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bq4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CYC3B_DESAF CYC3B_DESAF]] Exchanges electrons with [NiFe] and [Fe] hydrogenases and with the acidic cytochrome c3. Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.<ref>PMID:8573595</ref>	+	[https://www.uniprot.org/uniprot/CYC3B_DESAF CYC3B_DESAF] Exchanges electrons with [NiFe] and [Fe] hydrogenases and with the acidic cytochrome c3. Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.<ref>PMID:8573595</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio~~ africanus]]	+	[[Category: Desulfocurvibacter africanus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Czjzek, M]]	+	[[Category: Czjzek M]]
-	[[Category: Guerlesquin, F]]	+	[[Category: Guerlesquin F]]
-	[[Category: Hatchikian~~, E C~~]]	+	[[Category: Hatchikian EC]]
-	[[Category: Morelli, X]]	+	[[Category: Morelli X]]
-	[[Category: Pieulle, L]]	+	[[Category: Pieulle L]]
-	~~[[Category: Basic cytochrome c3]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Sad]]~~	+
-	~~[[Category: Sulfate reducing bacteria~~]]	+

OCA at 13:15, 24 November 2021

OCA — Wed, 24 Nov 2021 13:15:42 GMT

←Older revision		Revision as of 13:15, 24 November 2021
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	<StructureSection load='2bq4' size='340' side='right'caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='2bq4' size='340' side='right'caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=CA:CALCIUM+ION'>CA</scene>, <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">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [~~http~~://pdbe.org/2bq4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2bq4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2bq4 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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [https://pdbe.org/2bq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [https://www.ebi.ac.uk/pdbsum/2bq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bq4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CYC3B_DESAF CYC3B_DESAF]] Exchanges electrons with [NiFe] and [Fe] hydrogenases and with the acidic cytochrome c3. Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.<ref>PMID:8573595</ref>	+	[[https://www.uniprot.org/uniprot/CYC3B_DESAF CYC3B_DESAF]] Exchanges electrons with [NiFe] and [Fe] hydrogenases and with the acidic cytochrome c3. Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.<ref>PMID:8573595</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:05, 19 February 2020

OCA — Wed, 19 Feb 2020 08:05:40 GMT

←Older revision		Revision as of 08:05, 19 February 2020
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	==Crystal structure of type I cytochrome c3 from Desulfovibrio africanus==		==Crystal structure of type I cytochrome c3 from Desulfovibrio africanus==
-	<StructureSection load='2bq4' size='340' side='right' caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>	+	<StructureSection load='2bq4' size='340' side='right'caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>
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	==See Also==		==See Also==
-	*[[Cytochrome c\|Cytochrome c]]	+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio africanus]]		[[Category: Desulfovibrio africanus]]
		+	[[Category: Large Structures]]
	[[Category: Czjzek, M]]		[[Category: Czjzek, M]]
	[[Category: Guerlesquin, F]]		[[Category: Guerlesquin, F]]

OCA at 06:30, 16 May 2018

OCA — Wed, 16 May 2018 06:30:09 GMT

←Older revision		Revision as of 06:30, 16 May 2018
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-	==~~CRYSTAL STRUCTURE OF TYPE~~ I ~~CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS~~==	+
		+	==Crystal structure of type I cytochrome c3 from Desulfovibrio africanus==
	<StructureSection load='2bq4' size='340' side='right' caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='2bq4' size='340' side='right' caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=CA:CALCIUM+ION'>CA</scene>, <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">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [http://pdbe.org/2bq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/2bq4 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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [http://pdbe.org/2bq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/2bq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2bq4 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/bq/2bq4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/2bq4_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 11:31, 9 February 2016

OCA — Tue, 09 Feb 2016 11:31:30 GMT

←Older revision		Revision as of 11:31, 9 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=2bq4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:46, 10 September 2015

OCA — Thu, 10 Sep 2015 21:46:43 GMT

←Older revision		Revision as of 21:46, 10 September 2015
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=CA:CALCIUM+ION'>CA</scene>, <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">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/2bq4 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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [http://pdbe.org/2bq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/2bq4 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2bq4" style="background-color:#fffaf0;"></div>

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

OCA at 06:31, 25 December 2014

OCA — Thu, 25 Dec 2014 06:31:38 GMT

←Older revision		Revision as of 06:31, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/2bq4 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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/2bq4 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYC3B_DESAF CYC3B_DESAF]] Exchanges electrons with [NiFe] and [Fe] hydrogenases and with the acidic cytochrome c3. Participates in sulfate respiration coupled with phosphorylation by transferring electrons from the enzyme dehydrogenase to ferredoxin.<ref>PMID:8573595</ref>
	== 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: Desulfovibrio africanus]]		[[Category: Desulfovibrio africanus]]
-	[[Category: Czjzek, M.]]	+	[[Category: Czjzek, M]]
-	[[Category: Guerlesquin, F.]]	+	[[Category: Guerlesquin, F]]
-	[[Category: Hatchikian, E C.]]	+	[[Category: Hatchikian, E C]]
-	[[Category: Morelli, X.]]	+	[[Category: Morelli, X]]
-	[[Category: Pieulle, L.]]	+	[[Category: Pieulle, L]]
	[[Category: Basic cytochrome c3]]		[[Category: Basic cytochrome c3]]
	[[Category: Electron transfer]]		[[Category: Electron transfer]]

OCA at 09:55, 29 September 2014

OCA — Mon, 29 Sep 2014 09:55:21 GMT

←Older revision		Revision as of 09:55, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2bq4.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF TYPE I CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS==
		+	<StructureSection load='2bq4' size='340' side='right' caption='[[2bq4]], [[Resolution\|resolution]] 1.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2bq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BQ4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a2i\|1a2i]], [[1e39\|1e39]], [[1gm4\|1gm4]], [[1gmb\|1gmb]], [[1gx7\|1gx7]], [[1gyo\|1gyo]], [[1i77\|1i77]], [[1it1\|1it1]], [[1j0o\|1j0o]], [[1j0p\|1j0p]], [[1jrx\|1jrx]], [[1jry\|1jry]], [[1jrz\|1jrz]], [[1kss\|1kss]], [[1ksu\|1ksu]], [[1lj1\|1lj1]], [[1m1p\|1m1p]], [[1m64\|1m64]], [[1mdv\|1mdv]], [[1p2e\|1p2e]], [[1p2h\|1p2h]], [[1q9i\|1q9i]], [[1qjd\|1qjd]], [[1qn0\|1qn0]], [[1qn1\|1qn1]], [[1qo8\|1qo8]], [[1up9\|1up9]], [[1upd\|1upd]], [[1w7o\|1w7o]], [[1wad\|1wad]], [[1wr5\|1wr5]], [[2bpn\|2bpn]], [[2cth\|2cth]], [[3cao\|3cao]], [[3car\|3car]], [[3cyr\|3cyr]]</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=2bq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bq4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2bq4 RCSB], [http://www.ebi.ac.uk/pdbsum/2bq4 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/bq/2bq4_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 ==
		+	In Desulfovibrio metabolism, periplasmic hydrogen oxidation is coupled to cytoplasmic sulfate reduction via transmembrane electron transfer complexes. Type II tetraheme cytochrome c3 (TpII-c3), nine-heme cytochrome c (9HcA) and 16-heme cytochrome c (HmcA) are periplasmic proteins associated to these membrane-bound redox complexes and exhibit analogous physiological function. Type I tetraheme cytochrome c3 (TpI-c3) is thought to act as a mediator for electron transfer from hydrogenase to these multihemic cytochromes. In the present work we have investigated Desulfovibrio africanus (Da) and Desulfovibrio vulgaris Hildenborough (DvH) TpI-c3/TpII-c3 complexes. Comparative kinetic experiments of Da TpI-c3 and TpII-c3 using electrochemistry confirm that TpI-c3 is much more efficient than TpII-c3 as an electron acceptor from hydrogenase (second order rate constant k = 9 x 10(8) M(-1) s(-1), K(m) = 0.5 microM as compared to k = 1.7 x 10(7) M(-1) s(-1), K(m) = 40 microM, for TpI-c3 and TpII-c3, respectively). The Da TpI-c3/TpII-c3 complex was characterized at low ionic strength by gel filtration, analytical ultracentrifugation and cross-linking experiments. The thermodynamic parameters were determined by isothermal calorimetry titrations. The formation of the complex is mainly driven by a positive entropy change (deltaS = 137(+/-7) J mol(-1) K(-1) and deltaH = 5.1(+/-1.3) kJ mol(-1)) and the value for the association constant is found to be (2.2(+/-0.5)) x 10(6) M(-1) at pH 5.5. Our thermodynamic results reveal that the net increase in enthalpy and entropy is dominantly produced by proton release in combination with water molecule exclusion. Electrostatic forces play an important role in stabilizing the complex between the two proteins, since no complex formation is detected at high ionic strength. The crystal structure of Da TpI-c3 has been solved at 1.5 angstroms resolution and structural models of the complex have been obtained by NMR and docking experiments. Similar experiments have been carried out on the DvH TpI-c3/TpII-c3 complex. In both complexes, heme IV of TpI-c3 faces heme I of TpII-c3 involving basic residues of TpI-c3 and acidic residues of TpII-c3. A secondary interacting site has been observed in the two complexes, involving heme II of Da TpII-c3 and heme III of DvH TpI-c3 giving rise to a TpI-c3/TpII-c3 molar ratio of 2:1 and 1:2 for Da and DvH complexes, respectively. The physiological significance of these alternative sites in multiheme cytochromes c is discussed.

-	~~{{STRUCTURE_2bq4\| PDB=2bq4 \| SCENE= }}~~	+	The type I/type II cytochrome c3 complex: an electron transfer link in the hydrogen-sulfate reduction pathway.,Pieulle L, Morelli X, Gallice P, Lojou E, Barbier P, Czjzek M, Bianco P, Guerlesquin F, Hatchikian EC J Mol Biol. 2005 Nov 18;354(1):73-90. Epub 2005 Sep 29. PMID:16226767<ref>PMID:16226767</ref>

-	~~===CRYSTAL STRUCTURE OF TYPE I CYTOCHROME C3 FROM DESULFOVIBRIO AFRICANUS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16226767}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2bq4]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c\|Cytochrome c]]		*[[Cytochrome c\|Cytochrome c]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:016226767<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Desulfovibrio africanus]]		[[Category: Desulfovibrio africanus]]
	[[Category: Czjzek, M.]]		[[Category: Czjzek, M.]]

OCA at 13:42, 20 October 2012

OCA — Sat, 20 Oct 2012 13:42:02 GMT

←Older revision		Revision as of 13:42, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2bq4]] is a 2 chain structure ~~of [[Cytochrome c]]~~ with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA].	+	[[2bq4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BQ4 OCA].

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

OCA: Protected "2bq4" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 12:48:44 GMT

Protected "2bq4" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:48, 26 July 2012