1xme - Revision history

OCA at 06:47, 23 August 2023

OCA — Wed, 23 Aug 2023 06:47:32 GMT

←Older revision		Revision as of 06:47, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1xme' size='340' side='right'caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1xme' size='340' side='right'caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XME FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.3Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [https://pdbe.org/1xme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [https://www.ebi.ac.uk/pdbsum/1xme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xme ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [~~http~~://pdbe.org/1xme PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xme PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xme ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~COX2_THETH COX2_THETH~~]~~] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).~~	+	[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: Cytochrome-c oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen, Y]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Fee~~, J A~~]]	+	[[Category: Chen Y]]
-	[[Category: Hunsicker-Wang~~, L M~~]]	+	[[Category: Fee JA]]
-	[[Category: Pacoma~~, R L~~]]	+	[[Category: Hunsicker-Wang LM]]
-	[[Category: Stout~~, C D]]~~	+	[[Category: Pacoma RL]]
-	~~[[Category: Cytochrome oxidase]]~~	+	[[Category: Stout CD]]
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Heme-a]]~~	+
-	~~[[Category: Integral membrane protein]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:07, 6 January 2021

OCA — Wed, 06 Jan 2021 10:07:46 GMT

←Older revision		Revision as of 10:07, 6 January 2021
Line 1:		Line 1:

	==Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus==		==Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus==
-	<StructureSection load='1xme' size='340' side='right' caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1xme' size='340' side='right'caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XME FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://pdbe.org/1xme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xme ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://pdbe.org/1xme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xme ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Cytochrome c oxidase\|Cytochrome c oxidase]]	+	*[[Cytochrome c oxidase 3D structures\|Cytochrome c oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
	[[Category: Fee, J A]]		[[Category: Fee, J A]]

OCA at 07:03, 18 April 2018

OCA — Wed, 18 Apr 2018 07:03:18 GMT

←Older revision		Revision as of 07:03, 18 April 2018
Line 1:		Line 1:
		+
	==Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus==		==Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus==
	<StructureSection load='1xme' size='340' side='right' caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1xme' size='340' side='right' caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://pdbe.org/1xme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme 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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://pdbe.org/1xme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xme ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xm/1xme_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xm/1xme_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 07:18, 8 February 2016

OCA — Mon, 08 Feb 2016 07:18:11 GMT

←Older revision		Revision as of 07:18, 8 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xme ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:11, 10 September 2015

OCA — Thu, 10 Sep 2015 09:11:19 GMT

←Older revision		Revision as of 09:11, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1xme' size='340' side='right' caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1xme' size='340' side='right' caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XME FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XME FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 ~~Thermus thermophilus~~]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 ~~Thermus thermophilus~~]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 ~~Thermus thermophilus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme 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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://pdbe.org/1xme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1xme" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]
	[[Category: Fee, J A]]		[[Category: Fee, J A]]

OCA at 21:36, 24 December 2014

OCA — Wed, 24 Dec 2014 21:36:16 GMT

←Older revision		Revision as of 21:36, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XME FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XME FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme 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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COX2_THETH COX2_THETH]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Chen, Y.]]	+	[[Category: Chen, Y]]
-	[[Category: Fee, J A.]]	+	[[Category: Fee, J A]]
-	[[Category: Hunsicker-Wang, L M.]]	+	[[Category: Hunsicker-Wang, L M]]
-	[[Category: Pacoma, R L.]]	+	[[Category: Pacoma, R L]]
-	[[Category: Stout, C D.]]	+	[[Category: Stout, C D]]
	[[Category: Cytochrome oxidase]]		[[Category: Cytochrome oxidase]]
	[[Category: Heme]]		[[Category: Heme]]

OCA at 23:47, 28 September 2014

OCA — Sun, 28 Sep 2014 23:47:16 GMT

←Older revision		Revision as of 23:47, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1xme.~~png~~\|~~left~~\|200px]]	+	==Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus==
		+	<StructureSection load='1xme' size='340' side='right' caption='[[1xme]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XME FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaB, ctaC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></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=1xme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xme OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xme RCSB], [http://www.ebi.ac.uk/pdbsum/1xme 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/xm/1xme_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 ==
		+	Cytochrome ba(3) oxidase is an integral membrane protein identified in the thermophilic bacterium Thermus thermophilus. The enzyme has now been expressed recombinantly and purified with a histidine tag. As such, it crystallizes under similar conditions and in the same space group (P4(3)2(1)2) as the native protein. A novel cryoprotection scheme is described here to obtain high-resolution diffraction from these crystals, which involves soaking in a mixture of glycerol and ethylene glycol under a layer of oil. The unit-cell parameters for these crystals are larger than the native protein, apparently deriving from increased ordering of the N-terminus and an internal loop (residues 495-500) in subunit I. Hence, compared with native cytochrome ba(3) oxidase, the recombinant His-tagged protein is accommodated in an expanded but equally well ordered lattice via an alternate set of specific intermolecular contacts. The structure was refined against data to 2.3 angstroms resolution to an R factor of 21.7% and an R(free) of 23.7%.

-	~~{{STRUCTURE_1xme\| PDB=1xme \| SCENE= }}~~	+	A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus.,Hunsicker-Wang LM, Pacoma RL, Chen Y, Fee JA, Stout CD Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):340-3. Epub 2005, Feb 24. PMID:15735345<ref>PMID:15735345</ref>

-	~~===Structure~~ of ~~Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15735345}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1xme]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c oxidase\|Cytochrome c oxidase]]		*[[Cytochrome c oxidase\|Cytochrome c oxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015735345<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 09:21, 20 October 2012

OCA — Sat, 20 Oct 2012 09:21:55 GMT

←Older revision		Revision as of 09:21, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1xme]] is a 3 chain structure ~~of [[Cytochrome c oxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA].	+	[[1xme]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA].

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

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

OCA — Wed, 25 Jul 2012 22:37:42 GMT

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

←Older revision

Revision as of 22:37, 25 July 2012

OCA at 22:37, 25 July 2012

OCA — Wed, 25 Jul 2012 22:37:40 GMT

←Older revision		Revision as of 22:37, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1xme.png\|left\|200px]]		[[Image:1xme.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1xme", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1xme\| PDB=1xme \| SCENE= }}		{{STRUCTURE_1xme\| PDB=1xme \| SCENE= }}

	===Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus===		===Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15735345}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15735345 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15735345}}		{{ABSTRACT_PUBMED_15735345}}

	==About this Structure==		==About this Structure==
-	~~1XME~~ is a 3 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA].	+	[[1xme]] is a 3 chain structure of [[Cytochrome c oxidase]] with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XME OCA].
		+
		+	==See Also==
		+	*[[Cytochrome c oxidase\|Cytochrome c oxidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15735345~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015735345</ref><references group="xtra"/>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
Line 35:		Line 26:
	[[Category: Heme-a]]		[[Category: Heme-a]]
	[[Category: Integral membrane protein]]		[[Category: Integral membrane protein]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 20:07:45 2009''~~	+