3s38 - Revision history

OCA at 12:44, 14 March 2024

OCA — Thu, 14 Mar 2024 12:44:54 GMT

←Older revision		Revision as of 12:44, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3s38' size='340' side='right'caption='[[3s38]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='3s38' size='340' side='right'caption='[[3s38]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s38]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S38 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S38 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s38]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S38 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S38 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</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]] 4.2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaa ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbab, cbac ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbad ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [https://pdbe.org/3s38 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [https://www.ebi.ac.uk/pdbsum/3s38 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s38 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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [https://pdbe.org/3s38 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [https://www.ebi.ac.uk/pdbsum/3s38 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s38 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~COX2_THET8 COX2_THET8~~]~~] 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]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	We use a form of "freeze-trap, kinetic-crystallography" to explore the migration of Xe atoms away from the dinuclear heme-a3/CuB center in Thermus thermophilus cytochrome ba3 oxidase. This enzyme is a member of the heme-copper oxidase super-family, and is thus crucial for dioxygen dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O2 diffusion channel in cytochrome ba3 oxidase that is continuous, Y-shaped, 18-20 A in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a3-CuB center in the active site. To understand movement of gas molecules within the O2 channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 seconds while undergoing out-gassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 --> Xe5 --> Xe3 --> Xe4 sites, suggesting that ingress of O2 is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.	+
-		+
-	~~Mobility of Xe atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase.,Luna VM, Fee JA, Deniz AA, Stout CD Biochemistry. 2012 May 19. PMID:22607023<ref>PMID:22607023</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3s38" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Cytochrome c oxidase 3D structures\|Cytochrome c oxidase 3D structures]]		*[[Cytochrome c oxidase 3D structures\|Cytochrome c oxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cytochrome-c oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet8~~]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Deniz~~, A A~~]]	+	[[Category: Deniz AA]]
-	[[Category: Fee~~, J A~~]]	+	[[Category: Fee JA]]
-	[[Category: Luna~~, V M~~]]	+	[[Category: Luna VM]]
-	[[Category: Stout~~, C D]]~~	+	[[Category: Stout CD]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Xenon~~]]	+

OCA at 10:36, 22 June 2022

OCA — Wed, 22 Jun 2022 10:36:16 GMT

←Older revision		Revision as of 10:36, 22 June 2022
Line 1:		Line 1:

	==Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization==		==Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization==
-	<StructureSection load='3s38' size='340' side='right' caption='[[3s38]], [[Resolution\|resolution]] 4.20Å' scene=''>	+	<StructureSection load='3s38' size='340' side='right'caption='[[3s38]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s38]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S38 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S38 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s38]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S38 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S38 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</div></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=300852 THET8]), cbab, cbac ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbad ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbaa ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbab, cbac ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbad ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [~~http~~://pdbe.org/3s38 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s38 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s38 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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [https://pdbe.org/3s38 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [https://www.ebi.ac.uk/pdbsum/3s38 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s38 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/COX2_THET8 COX2_THET8]] 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/COX2_THET8 COX2_THET8]] 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).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:

	==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 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Thet8]]		[[Category: Thet8]]
	[[Category: Deniz, A A]]		[[Category: Deniz, A A]]

OCA at 03:39, 5 August 2016

OCA — Fri, 05 Aug 2016 03:39:00 GMT

←Older revision		Revision as of 03:39, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization==		==Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization==
	<StructureSection load='3s38' size='340' side='right' caption='[[3s38]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='3s38' size='340' side='right' caption='[[3s38]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s38]] 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=3S38 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S38 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s38]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S38 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S38 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</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, cbac ([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=300852 THET8]), cbab, cbac ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), cbad ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [http://www.ebi.ac.uk/pdbsum/3s38 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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [http://pdbe.org/3s38 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [http://www.ebi.ac.uk/pdbsum/3s38 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s38 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	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 3s38" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 27:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Thet8]]
	[[Category: Deniz, A A]]		[[Category: Deniz, A A]]
	[[Category: Fee, J A]]		[[Category: Fee, J A]]

OCA at 22:36, 24 December 2014

OCA — Wed, 24 Dec 2014 22:36:14 GMT

←Older revision		Revision as of 22:36, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3s38]] 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=3S38 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S38 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3s38]] 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=3S38 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S38 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</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, cbac ([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, cbac ([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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [http://www.ebi.ac.uk/pdbsum/3s38 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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [http://www.ebi.ac.uk/pdbsum/3s38 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COX2_THET8 COX2_THET8]] 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).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 28:
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Deniz, A A.]]	+	[[Category: Deniz, A A]]
-	[[Category: Fee, J A.]]	+	[[Category: Fee, J A]]
-	[[Category: Luna, V M.]]	+	[[Category: Luna, V M]]
-	[[Category: Stout, C D.]]	+	[[Category: Stout, C D]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Xenon]]		[[Category: Xenon]]

OCA at 10:23, 16 June 2014

OCA — Mon, 16 Jun 2014 10:23:20 GMT

←Older revision		Revision as of 10:23, 16 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3s38.~~png~~\|~~left~~\|~~200px~~]]	+	==Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization==
		+	<StructureSection load='3s38' size='340' side='right' caption='[[3s38]], [[Resolution\|resolution]] 4.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s38]] 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=3S38 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S38 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3s33\|3s33]], [[3s39\|3s39]], [[3s3a\|3s3a]], [[3s3b\|3s3b]], [[3s3c\|3s3c]], [[3s3d\|3s3d]]</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, cbac ([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=3s38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s38 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s38 RCSB], [http://www.ebi.ac.uk/pdbsum/3s38 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	We use a form of "freeze-trap, kinetic-crystallography" to explore the migration of Xe atoms away from the dinuclear heme-a3/CuB center in Thermus thermophilus cytochrome ba3 oxidase. This enzyme is a member of the heme-copper oxidase super-family, and is thus crucial for dioxygen dependent life. The mechanisms involved in the migration of oxygen, water, electrons, and protons into and/or out of the specialized channels of the heme-copper oxidases are generally not well understood. Pressurization of crystals with Xe gas previously revealed a O2 diffusion channel in cytochrome ba3 oxidase that is continuous, Y-shaped, 18-20 A in length and comprised of hydrophobic residues, connecting the protein surface within the bilayer to the a3-CuB center in the active site. To understand movement of gas molecules within the O2 channel, we performed crystallographic analysis of 19 Xe laden crystals freeze-trapped in liquid nitrogen at selected times between 0 and 480 seconds while undergoing out-gassing at room temperature. Variation in Xe crystallographic occupancy at five discrete sites as a function of time leads to a kinetic model revealing relative degrees of mobility of Xe atoms within the channel. Xe egress occurs primarily through the channel formed by the Xe1 --> Xe5 --> Xe3 --> Xe4 sites, suggesting that ingress of O2 is likely to occur by the reverse of this process. The channel itself appears not to undergo significant structural changes during Xe migration, thereby indicating a passive role in this important physiological function.

-	~~{{STRUCTURE_3s38\| PDB=3s38 \| SCENE= }}~~	+	Mobility of Xe atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase.,Luna VM, Fee JA, Deniz AA, Stout CD Biochemistry. 2012 May 19. PMID:22607023<ref>PMID:22607023</ref>

-	~~===Structure~~ of ~~Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22607023}}~~	+	==See Also==
-		+	*[[Cytochrome c oxidase\|Cytochrome c oxidase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~3s38~~]] 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=3S38 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:022607023<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 05:26, 12 September 2012

OCA — Wed, 12 Sep 2012 05:26:13 GMT

←Older revision		Revision as of 05:26, 12 September 2012
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	[[Image:3s38.png\|left\|200px]]		[[Image:3s38.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3s38\| PDB=3s38 \| SCENE= }}		{{STRUCTURE_3s38\| PDB=3s38 \| SCENE= }}

	===Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization===		===Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_22607023}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 22607023 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_22607023}}		{{ABSTRACT_PUBMED_22607023}}

OCA at 04:53, 30 May 2012

OCA — Wed, 30 May 2012 04:53:42 GMT

←Older revision		Revision as of 04:53, 30 May 2012
Line 1:		Line 1:
-	[[Image:3s38.~~jpg~~\|left\|200px]]	+	[[Image:3s38.png\|left\|200px]]

	<!--		<!--
Line 11:		Line 11:
	===Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization===		===Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22607023}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22607023 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22607023}}

	==About this Structure==		==About this Structure==
	[[3s38]] 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=3S38 OCA].		[[3s38]] 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=3S38 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022607023</ref><references group="xtra"/>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA at 06:10, 23 May 2012

OCA — Wed, 23 May 2012 06:10:18 GMT

←Older revision		Revision as of 06:10, 23 May 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3s38.jpg\|left\|200px]]

-	The ~~entry 3s38~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s38", 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_3s38\| PDB=3s38 \| SCENE= }}

-	~~Authors: Luna, V.M., Fee, J.A., Deniz, A.A., Stout, C.D.~~	+	===Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization===

-	~~Description:~~ Structure of Thermus thermophilus ~~cytochrome ba3~~ oxidase ~~30s after Xe depressurization~~	+
		+	==About this Structure==
		+	[[3s38]] 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=3S38 OCA].
		+	[[Category: Cytochrome-c oxidase]]
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Deniz, A A.]]
		+	[[Category: Fee, J A.]]
		+	[[Category: Luna, V M.]]
		+	[[Category: Stout, C D.]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Xenon]]

OCA at 04:52, 8 June 2011

OCA — Wed, 08 Jun 2011 04:52:25 GMT

←Older revision		Revision as of 04:52, 8 June 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s38 is ON HOLD	+	The entry 3s38 is ON HOLD until Paper Publication

	Authors: Luna, V.M., Fee, J.A., Deniz, A.A., Stout, C.D.		Authors: Luna, V.M., Fee, J.A., Deniz, A.A., Stout, C.D.

	Description: Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization		Description: Structure of Thermus thermophilus cytochrome ba3 oxidase 30s after Xe depressurization

OCA: Protected "3s38" [edit=sysop:move=sysop]

OCA — Wed, 25 May 2011 05:15:27 GMT

Protected "3s38" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:15, 25 May 2011