2zfe - Revision history

OCA at 13:34, 1 November 2023

OCA — Wed, 01 Nov 2023 13:34:58 GMT

←Older revision		Revision as of 13:34, 1 November 2023
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	<StructureSection load='2zfe' size='340' side='right'caption='[[2zfe]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2zfe' size='340' side='right'caption='[[2zfe]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Halobacterium_salinarium~~ Halobacterium ~~salinarium~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=~~RET~~:~~RETINAL~~'>~~RET~~</scene>, <scene name='pdbligand=XE:~~XENON~~'>XE</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA~~-~~D-MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~SGA~~:~~O3-SULFONYLGALACTOSE~~'>~~SGA~~</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]] 2.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [~~http~~://pdbe.org/2zfe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zfe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfe 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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [https://pdbe.org/2zfe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [https://www.ebi.ac.uk/pdbsum/2zfe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.	+	[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Halobacterium ~~salinarium~~]]	+	[[Category: Halobacterium salinarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kouyama, T]]	+	[[Category: Kouyama T]]
-	~~[[Category: Chromophore]]~~	+
-	~~[[Category: Hydrogen ion transport]]~~	+
-	~~[[Category: Hydrophobic cavity]]~~	+
-	~~[[Category: Ion transport]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Photoreceptor protein]]~~	+
-	~~[[Category: Proton transport]]~~	+
-	~~[[Category: Pyrrolidone carboxylic acid]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Retinal protein]]~~	+
-	~~[[Category: Sensory transduction]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 12:03, 29 July 2020

OCA — Wed, 29 Jul 2020 12:03:45 GMT

←Older revision		Revision as of 12:03, 29 July 2020
Line 1:		Line 1:

	==Crystal structure of bacteriorhodopsin-xenon complex==		==Crystal structure of bacteriorhodopsin-xenon complex==
-	<StructureSection load='2zfe' size='340' side='right' caption='[[2zfe]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2zfe' size='340' side='right'caption='[[2zfe]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarium Halobacterium salinarium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarium Halobacterium salinarium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D-MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~RET~~:~~RETINAL~~'>~~RET~~</scene>, <scene name='pdbligand=~~SGA~~:O3-~~SULFONYLGALACTOSE~~'>~~SGA~~</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=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=XE:XENON'>XE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://pdbe.org/2zfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfe 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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://pdbe.org/2zfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]	+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Halobacterium salinarium]]		[[Category: Halobacterium salinarium]]
		+	[[Category: Large Structures]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Chromophore]]		[[Category: Chromophore]]

OCA at 07:00, 18 October 2018

OCA — Thu, 18 Oct 2018 07:00:11 GMT

←Older revision		Revision as of 07:00, 18 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of bacteriorhodopsin-xenon complex==		==Crystal structure of bacteriorhodopsin-xenon complex==
	<StructureSection load='2zfe' size='340' side='right' caption='[[2zfe]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2zfe' size='340' side='right' caption='[[2zfe]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Halobacterium_salinarum~~ Halobacterium ~~salinarum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarium Halobacterium salinarium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=~~RET~~:~~RETINAL~~'>~~RET~~</scene>, <scene name='pdbligand=XE:~~XENON~~'>XE</scene>, <scene name='pdbligand=~~MAN~~:~~ALPHA-D~~-~~MANNOSE~~'>~~MAN~~</scene>, <scene name='pdbligand=~~SGA~~:~~O3-SULFONYLGALACTOSE~~'>~~SGA~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</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">[[1iw6\|1iw6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://pdbe.org/2zfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe 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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://pdbe.org/2zfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zfe 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/zf/2zfe_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zf/2zfe_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 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Halobacterium ~~salinarum~~]]	+	[[Category: Halobacterium salinarium]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Chromophore]]		[[Category: Chromophore]]

OCA at 06:29, 7 February 2016

OCA — Sun, 07 Feb 2016 06:29:09 GMT

←Older revision		Revision as of 06:29, 7 February 2016
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=XE:XENON'>XE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=XE:XENON'>XE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe 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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://pdbe.org/2zfe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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=2zfe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2zfe" style="background-color:#fffaf0;"></div>

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

OCA at 08:37, 24 December 2014

OCA — Wed, 24 Dec 2014 08:37:56 GMT

←Older revision		Revision as of 08:37, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=XE:XENON'>XE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=XE:XENON'>XE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe 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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
-	[[Category: Kouyama, T.]]	+	[[Category: Kouyama, T]]
	[[Category: Chromophore]]		[[Category: Chromophore]]
	[[Category: Hydrogen ion transport]]		[[Category: Hydrogen ion transport]]

OCA at 08:34, 29 September 2014

OCA — Mon, 29 Sep 2014 08:34:30 GMT

←Older revision		Revision as of 08:34, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2zfe.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of bacteriorhodopsin-xenon complex==
		+	<StructureSection load='2zfe' size='340' side='right' caption='[[2zfe]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZFE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=L1P:3-PHOSPHORYL-[1,2-DI-PHYTANYL]GLYCEROL'>L1P</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=L3P:2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3-SN-GLYCEROL-1-PHOSPHATE'>L3P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=XE:XENON'>XE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=SGA:O3-SULFONYLGALACTOSE'>SGA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]]</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=2zfe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zfe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zfe RCSB], [http://www.ebi.ac.uk/pdbsum/2zfe 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/zf/2zfe_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 ==
		+	To understand the functional role of apolar cavities in bacteriorhodopsin, a light-driven proton pump found in Halobacterium salinarum, we investigated the crystal structure in pressurized xenon or krypton. Diffraction data from the P622 crystal showed that one Xe or Kr atom binds to a preexisting hydrophobic cavity buried between helices C and D, located at the same depth from the membrane surface as Asp96, a key residue in the proton uptake pathway. The occupation fraction of Xe or Kr was calculated as approximately 0.32 at a pressure of 1 MPa. In the unphotolyzed state, the binding of Xe or Kr caused no large deformation of the cavity. However, the proton pumping cycle was greatly perturbed when an aqueous suspension of purple membrane was pressurized with xenon gas; that is, the decay of the M state was accelerated significantly (~5 times at full occupancy), while the decay of an equilibrium state of N and O was slightly decelerated. A similar but much smaller perturbation in the reaction kinetics was observed upon pressurization with krypton gas. In a glycerol/water mixture, xenon-induced acceleration of M decay became less significant in proportion to the water activity. Together with the structure of the xenon-bound protein, these observations suggest that xenon binding helps water molecules permeate into apolar cavities in the proton uptake pathway, thereby accelerating the water-mediated proton transfer from Asp96 to the Schiff base.

-	~~{{STRUCTURE_2zfe\| PDB=2zfe \| SCENE= }}~~	+	Effect of xenon binding to a hydrophobic cavity on the proton pumping cycle in bacteriorhodopsin.,Hayakawa N, Kasahara T, Hasegawa D, Yoshimura K, Murakami M, Kouyama T J Mol Biol. 2008 Dec 26;384(4):812-23. Epub 2008 Oct 9. PMID:18930734<ref>PMID:18930734</ref>

-	~~===Crystal structure~~ of ~~bacteriorhodopsin-xenon complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18930734}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2zfe]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Halobacterium_salinarum Halobacterium salinarum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].~~	+

	==See Also==		==See Also==
	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]		*[[Bacteriorhodopsin\|Bacteriorhodopsin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018930734<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]

OCA at 05:51, 20 October 2012

OCA — Sat, 20 Oct 2012 05:51:13 GMT

←Older revision		Revision as of 05:51, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2zfe]] is a 1 chain structure ~~of [[Bacteriorhodopsin]]~~ with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].	+	[[2zfe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].

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

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

OCA — Wed, 25 Jul 2012 11:20:27 GMT

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

←Older revision

Revision as of 11:20, 25 July 2012

OCA at 11:20, 25 July 2012

OCA — Wed, 25 Jul 2012 11:20:25 GMT

←Older revision		Revision as of 11:20, 25 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2zfe.png\|left\|200px]]		[[Image:2zfe.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zfe", 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_2zfe\| PDB=2zfe \| SCENE= }}		{{STRUCTURE_2zfe\| PDB=2zfe \| SCENE= }}

	===Crystal structure of bacteriorhodopsin-xenon complex===		===Crystal structure of bacteriorhodopsin-xenon complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18930734}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18930734 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18930734}}		{{ABSTRACT_PUBMED_18930734}}

	==About this Structure==		==About this Structure==
-	~~2ZFE~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].	+	[[2zfe]] is a 1 chain structure of [[Bacteriorhodopsin]] with sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18930734~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018930734</ref><references group="xtra"/>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]
Line 39:		Line 30:
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Transport]]		[[Category: Transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:57:48 2009''

OCA at 09:57, 16 February 2009

OCA — Mon, 16 Feb 2009 09:57:49 GMT

←Older revision		Revision as of 09:57, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2ZFE is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].	+	2ZFE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Halobacterium_salinarum Halobacterium salinarum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZFE OCA].

	==Reference==		==Reference==
-	~~Effect of Xenon Binding to a Hydrophobic Cavity on the Proton Pumping Cycle in Bacteriorhodopsin., Hayakawa N, Kasahara T, Hasegawa D, Yoshimura K, Murakami M, Kouyama T, J Mol Biol. 2008 Oct 9.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18930734 18930734]~~	+	<ref group="xtra">PMID:18930734</ref><references group="xtra"/>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
-	[[Category: ~~Single protein]]~~	+	[[Category: Kouyama, T.]]
-	~~[[Category: Pdbx_ordinal=~~, ~~<PDBx:audit_author~~.]]	+
	[[Category: Chromophore]]		[[Category: Chromophore]]
	[[Category: Hydrogen ion transport]]		[[Category: Hydrogen ion transport]]
Line 41:		Line 40:
	[[Category: Transport]]		[[Category: Transport]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Dec 10 20~~:35:~~41 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:57:48 2009''