1dw0 - Revision history

OCA at 09:54, 20 March 2024

OCA — Wed, 20 Mar 2024 09:54:38 GMT

←Older revision		Revision as of 09:54, 20 March 2024
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	<StructureSection load='1dw0' size='340' side='right'caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='1dw0' size='340' side='right'caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Rhodobacter_sphaeroides Rhodobacter~~ sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides Cereibacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW0 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>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.82Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1dw1\|1dw1]]~~, ~~[[1dw2\|1dw2]], [[1dw3\|1dw3]]~~</~~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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [https://pdbe.org/1dw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw0 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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [https://pdbe.org/1dw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~SHP_RHOS4 SHP_RHOS4]~~] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.	+	[https://www.uniprot.org/uniprot/SHP_CERS4 SHP_CERS4] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.
	== 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=1dw0 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=1dw0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The photosynthetic bacterium Rhodobacter sphaeroides produces a heme protein (SHP), which is an unusual c-type cytochrome capable of transiently binding oxygen during autooxidation. Similar proteins have not only been observed in other photosynthetic bacteria but also in the obligate methylotroph Methylophilus methylotrophus and the metal reducing bacterium Shewanella putrefaciens. A three-dimensional structure of SHP was derived using the multiple isomorphous replacement phasing method. Besides a model for the oxidized state (to 1.82 A resolution), models for the reduced state (2.1 A resolution), the oxidized molecule liganded with cyanide (1. 90 A resolution), and the reduced molecule liganded with nitric oxide (2.20 A resolution) could be derived. The SHP structure represents a new variation of the class I cytochrome c fold. The oxidized state reveals a novel sixth heme ligand, Asn(88), which moves away from the iron upon reduction or when small molecules bind. The distal side of the heme has a striking resemblance to other heme proteins that bind gaseous compounds. In SHP the liberated amide group of Asn(88) stabilizes solvent-shielded ligands through a hydrogen bond.
-
-	Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.,Leys D, Backers K, Meyer TE, Hagen WR, Cusanovich MA, Van Beeumen JJ J Biol Chem. 2000 May 26;275(21):16050-6. PMID:10821858<ref>PMID:10821858</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dw0" 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: Cereibacter sphaeroides]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Rhodobacter sphaeroides]]~~	+	[[Category: Backers K]]
-	[[Category: Backers, K]]	+	[[Category: Cusanovich MA]]
-	~~[[Category: Beeumen, J J.Van~~]]	+	[[Category: Hagen WR]]
-	[[Category: Cusanovich~~, M A~~]]	+	[[Category: Leys D]]
-	[[Category: Hagen~~, W R~~]]	+	[[Category: Meyer TE]]
-	[[Category: Leys, D]]	+	[[Category: Van Beeumen JJ]]
-	[[Category: Meyer~~, T E~~]]	+
-	[[Category: ~~Asparagine ligation]]~~	+
-	~~[[Category: Cytochrome c]]~~	+
-	~~[[Category: Disulfide bridge]]~~	+
-	~~[[Category: Oxygen binding]]~~	+
-	~~[[Category: Oxygen storage-transport complex~~]]	+

OCA at 14:48, 3 March 2021

OCA — Wed, 03 Mar 2021 14:48:50 GMT

←Older revision		Revision as of 14:48, 3 March 2021
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	<StructureSection load='1dw0' size='340' side='right'caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='1dw0' size='340' side='right'caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~HEM~~:~~PROTOPORPHYRIN+IX+CONTAINING~~+FE'>~~HEM~~</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [~~http~~://pdbe.org/1dw0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dw0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw0 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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [https://pdbe.org/1dw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw0 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SHP_RHOS4 SHP_RHOS4]] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.	+	[[https://www.uniprot.org/uniprot/SHP_RHOS4 SHP_RHOS4]] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:24, 16 October 2019

OCA — Wed, 16 Oct 2019 11:24:09 GMT

←Older revision		Revision as of 11:24, 16 October 2019
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	==STRUCTURE OF OXIDIZED SHP, AN OXYGEN BINDING CYTOCHROME C==		==STRUCTURE OF OXIDIZED SHP, AN OXYGEN BINDING CYTOCHROME C==
-	<StructureSection load='1dw0' size='340' side='right' caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>	+	<StructureSection load='1dw0' size='340' side='right'caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1dw0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1dw0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	[[Category: Backers, K]]		[[Category: Backers, K]]

OCA at 08:04, 13 December 2017

OCA — Wed, 13 Dec 2017 08:04:53 GMT

←Older revision		Revision as of 08:04, 13 December 2017
Line 1:		Line 1:
		+
	==STRUCTURE OF OXIDIZED SHP, AN OXYGEN BINDING CYTOCHROME C==		==STRUCTURE OF OXIDIZED SHP, AN OXYGEN BINDING CYTOCHROME C==
	<StructureSection load='1dw0' size='340' side='right' caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='1dw0' size='340' side='right' caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://pdbe.org/1dw0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://pdbe.org/1dw0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw0 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/dw/1dw0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/1dw0_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 1dw0" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1dw0" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome c\|Cytochrome c]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:33, 9 February 2016

OCA — Tue, 09 Feb 2016 20:33:10 GMT

←Older revision		Revision as of 20:33, 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=1dw0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:47, 11 September 2015

OCA — Fri, 11 Sep 2015 01:47:59 GMT

←Older revision		Revision as of 01:47, 11 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://pdbe.org/1dw0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 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 1dw0" style="background-color:#fffaf0;"></div>

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

OCA at 09:22, 25 December 2014

OCA — Thu, 25 Dec 2014 09:22:04 GMT

←Older revision		Revision as of 09:22, 25 December 2014
Line 7:		Line 7:
	<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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SHP_RHOS4 SHP_RHOS4]] High-spin cytochrome. Transiently bind oxygen during autoxidation, which occurs with a half-life of 3 min with a 4-fold excess of O(2). Also binds carbon monoxide, azide and cyanide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:04, 22 December 2014

OCA — Mon, 22 Dec 2014 22:04:24 GMT

←Older revision		Revision as of 22:04, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
-	[[Category: Backers, K.]]	+	[[Category: Backers, K]]
-	[[Category: Beeumen, J J.Van.]]	+	[[Category: Beeumen, J J.Van]]
-	[[Category: Cusanovich, M A.]]	+	[[Category: Cusanovich, M A]]
-	[[Category: Hagen, W R.]]	+	[[Category: Hagen, W R]]
-	[[Category: Leys, D.]]	+	[[Category: Leys, D]]
-	[[Category: Meyer, T E.]]	+	[[Category: Meyer, T E]]
	[[Category: Asparagine ligation]]		[[Category: Asparagine ligation]]
	[[Category: Cytochrome c]]		[[Category: Cytochrome c]]

OCA at 10:57, 10 September 2014

OCA — Wed, 10 Sep 2014 10:57:21 GMT

←Older revision		Revision as of 10:57, 10 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1dw0.~~png~~\|~~left~~\|200px]]	+	==STRUCTURE OF OXIDIZED SHP, AN OXYGEN BINDING CYTOCHROME C==
		+	<StructureSection load='1dw0' size='340' side='right' caption='[[1dw0]], [[Resolution\|resolution]] 1.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dw0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dw1\|1dw1]], [[1dw2\|1dw2]], [[1dw3\|1dw3]]</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=1dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw0 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw0 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/dw/1dw0_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 photosynthetic bacterium Rhodobacter sphaeroides produces a heme protein (SHP), which is an unusual c-type cytochrome capable of transiently binding oxygen during autooxidation. Similar proteins have not only been observed in other photosynthetic bacteria but also in the obligate methylotroph Methylophilus methylotrophus and the metal reducing bacterium Shewanella putrefaciens. A three-dimensional structure of SHP was derived using the multiple isomorphous replacement phasing method. Besides a model for the oxidized state (to 1.82 A resolution), models for the reduced state (2.1 A resolution), the oxidized molecule liganded with cyanide (1. 90 A resolution), and the reduced molecule liganded with nitric oxide (2.20 A resolution) could be derived. The SHP structure represents a new variation of the class I cytochrome c fold. The oxidized state reveals a novel sixth heme ligand, Asn(88), which moves away from the iron upon reduction or when small molecules bind. The distal side of the heme has a striking resemblance to other heme proteins that bind gaseous compounds. In SHP the liberated amide group of Asn(88) stabilizes solvent-shielded ligands through a hydrogen bond.

-	~~{{STRUCTURE_1dw0\| PDB=1dw0 \| SCENE= }}~~	+	Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.,Leys D, Backers K, Meyer TE, Hagen WR, Cusanovich MA, Van Beeumen JJ J Biol Chem. 2000 May 26;275(21):16050-6. PMID:10821858<ref>PMID:10821858</ref>

-	~~===STRUCTURE OF OXIDIZED SHP~~, ~~AN OXYGEN BINDING CYTOCHROME C===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10821858}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1dw0]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c\|Cytochrome c]]		*[[Cytochrome c\|Cytochrome c]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:010821858<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Rhodobacter sphaeroides]]		[[Category: Rhodobacter sphaeroides]]
	[[Category: Backers, K.]]		[[Category: Backers, K.]]

OCA at 15:03, 20 October 2012

OCA — Sat, 20 Oct 2012 15:03:04 GMT

←Older revision		Revision as of 15:03, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1dw0]] is a 3 chain structure ~~of [[Cytochrome c]]~~ with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA].	+	[[1dw0]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW0 OCA].

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