2zzl - Revision history

OCA at 14:04, 1 November 2023

OCA — Wed, 01 Nov 2023 14:04:06 GMT

←Older revision		Revision as of 14:04, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2zzl' size='340' side='right'caption='[[2zzl]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='2zzl' size='340' side='right'caption='[[2zzl]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2ZZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZZL 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=~~SOG~~:~~2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL~~'>~~SOG~~</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]] 2.03Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]], [[1iw9\|1iw9]]~~</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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [~~http~~://pdbe.org/2zzl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2zzl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2zzl 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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [https://pdbe.org/2zzl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [https://www.ebi.ac.uk/pdbsum/2zzl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zzl 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]]
Line 38:		Line 38:
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kouyama, T]]	+	[[Category: Kouyama T]]
-	[[Category: Yamamoto, M]]	+	[[Category: Yamamoto M]]
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Chromophore]]~~	+
-	~~[[Category: Hydrogen ion transport]]~~	+
-	~~[[Category: Ion transport]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Photoreceptor protein]]~~	+
-	~~[[Category: Protein-lipid complex]]~~	+
-	~~[[Category: Proton transport]]~~	+
-	~~[[Category: Pyrrolidone carboxylic acid]]~~	+
-	~~[[Category: Reaction intermediate]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Retinal]]~~	+
-	~~[[Category: Retinal protein]]~~	+
-	~~[[Category: Sensory transduction]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 12:12, 29 July 2020

OCA — Wed, 29 Jul 2020 12:12:19 GMT

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

	==Structure of bacteriorhodopsin's M intermediate at pH 7==		==Structure of bacteriorhodopsin's M intermediate at pH 7==
-	<StructureSection load='2zzl' size='340' side='right' caption='[[2zzl]], [[Resolution\|resolution]] 2.03Å' scene=''>	+	<StructureSection load='2zzl' size='340' side='right'caption='[[2zzl]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2ZZL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2ZZL 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=~~SOG~~:2-~~HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL~~'>~~SOG~~</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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</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]], [[1iw9\|1iw9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]], [[1iw9\|1iw9]]</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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://pdbe.org/2zzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zzl 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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://pdbe.org/2zzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zzl 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 salinarum]]		[[Category: Halobacterium salinarum]]
		+	[[Category: Large Structures]]
	[[Category: Kouyama, T]]		[[Category: Kouyama, T]]
	[[Category: Yamamoto, M]]		[[Category: Yamamoto, M]]

OCA at 07:31, 18 October 2018

OCA — Thu, 18 Oct 2018 07:31:33 GMT

←Older revision		Revision as of 07:31, 18 October 2018
Line 1:		Line 1:
		+
	==Structure of bacteriorhodopsin's M intermediate at pH 7==		==Structure of bacteriorhodopsin's M intermediate at pH 7==
	<StructureSection load='2zzl' size='340' side='right' caption='[[2zzl]], [[Resolution\|resolution]] 2.03Å' scene=''>		<StructureSection load='2zzl' size='340' side='right' caption='[[2zzl]], [[Resolution\|resolution]] 2.03Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZZL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZZL 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=~~SOG~~:~~2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL~~'>~~SOG~~</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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]], [[1iw9\|1iw9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]], [[1iw9\|1iw9]]</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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://pdbe.org/2zzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl 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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://pdbe.org/2zzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zzl 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/zz/2zzl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zz/2zzl_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 21:38, 7 February 2016

OCA — Sun, 07 Feb 2016 21:38:15 GMT

←Older revision		Revision as of 21:38, 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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</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]], [[1iw9\|1iw9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]], [[1iw9\|1iw9]]</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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl 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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://pdbe.org/2zzl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl 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=2zzl 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 2zzl" style="background-color:#fffaf0;"></div>

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

OCA at 18:24, 24 December 2014

OCA — Wed, 24 Dec 2014 18:24:18 GMT

←Older revision		Revision as of 18:24, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZZL FirstGlance]. <br>		<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZZL 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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</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]], [[1iw9\|1iw9]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iw6\|1iw6]], [[1iw9\|1iw9]]</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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl 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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl 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: Yamamoto, M.]]	+	[[Category: Yamamoto, M]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
	[[Category: Chromophore]]		[[Category: Chromophore]]

OCA at 08:12, 29 September 2014

OCA — Mon, 29 Sep 2014 08:12:14 GMT

←Older revision		Revision as of 08:12, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2zzl.~~png~~\|~~left~~\|200px]]	+	==Structure of bacteriorhodopsin's M intermediate at pH 7==
		+	<StructureSection load='2zzl' size='340' side='right' caption='[[2zzl]], [[Resolution\|resolution]] 2.03Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2zzl]] 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=2ZZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZZL 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=SOG:2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL'>SOG</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]], [[1iw9\|1iw9]]</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=2zzl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zzl RCSB], [http://www.ebi.ac.uk/pdbsum/2zzl 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/zz/2zzl_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The hexagonal P622 crystal of bacteriorhodopsin, which is made up of stacked membranes, is stable provided that the precipitant concentration in the soaking solution is higher than a critical value (i.e., 1.5 M ammonium sulfate). Diffraction data showed that the crystal lattice shrank linearly with increasing precipitant concentration, due primarily to narrowing of intermembrane spaces. Although the crystal shrinkage did not affect the rate of formation of the photoreaction M intermediate, its lifetime increased exponentially with the precipitant concentration. It was suggested that the energetic barrier of the M-to-N transition becomes higher when the motional freedom of the EF loop is reduced by crystal lattice force. As a result of this property, the M state accumulated predominantly when the crystal that was soaked at a high precipitant concentration was illuminated at room temperature. Structural data obtained at various pH levels showed that the overall structure of M is not strongly dependent on pH, except that Glu194 and Glu204 in the proton release complex are more separated at pH 7 than at pH 4.4. This result suggests that light-induced disruption of the paired structure of Glu194 and Glu204 is incomplete when external pH is lower than the pK(a) value of the proton release group in the M state.

-	~~{{STRUCTURE_2zzl\| PDB=2zzl \| SCENE= }}~~	+	Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels.,Yamamoto M, Hayakawa N, Murakami M, Kouyama T J Mol Biol. 2009 Oct 30;393(3):559-73. Epub 2009 Aug 25. PMID:19712684<ref>PMID:19712684</ref>

-	~~===Structure~~ of ~~bacteriorhodopsin's M intermediate at pH 7===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19712684}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2zzl]] 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=2ZZL OCA].~~	+

	==See Also==		==See Also==
	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]		*[[Bacteriorhodopsin\|Bacteriorhodopsin]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019712684<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]

OCA at 07:55, 20 October 2012

OCA — Sat, 20 Oct 2012 07:55:43 GMT

←Older revision		Revision as of 07:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2zzl]] 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=2ZZL OCA].	+	[[2zzl]] 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=2ZZL OCA].

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

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

OCA — Wed, 25 Jul 2012 17:54:46 GMT

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

←Older revision

Revision as of 17:54, 25 July 2012

OCA at 17:54, 25 July 2012

OCA — Wed, 25 Jul 2012 17:54:43 GMT

←Older revision		Revision as of 17:54, 25 July 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:2zzl.png\|left\|200px]]
-	[[Image:2zzl.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2zzl", 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_2zzl\| PDB=2zzl \| SCENE= }}		{{STRUCTURE_2zzl\| PDB=2zzl \| SCENE= }}

	===Structure of bacteriorhodopsin's M intermediate at pH 7===		===Structure of bacteriorhodopsin's M intermediate at pH 7===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19712684}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19712684 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19712684}}		{{ABSTRACT_PUBMED_19712684}}

	==About this Structure==		==About this Structure==
-	~~2ZZL~~ 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=2ZZL OCA].	+	[[2zzl]] 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=2ZZL OCA].
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin\|Bacteriorhodopsin]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19712684~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019712684</ref><references group="xtra"/>
	[[Category: Halobacterium salinarum]]		[[Category: Halobacterium salinarum]]
	[[Category: Kouyama, T.]]		[[Category: Kouyama, T.]]
Line 43:		Line 34:
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Transport]]		[[Category: Transport]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 7 13:58:29 2009''

OCA at 11:58, 7 October 2009

OCA — Wed, 07 Oct 2009 11:58:32 GMT

←Older revision		Revision as of 11:58, 7 October 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:2zzl.jpg\|left\|200px]]

-	The ~~entry 2zzl~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2zzl", 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_2zzl\| PDB=2zzl \| SCENE= }}

-	~~Authors: Yamamoto~~ M~~., Kouyama T.~~	+	===Structure of bacteriorhodopsin's M intermediate at pH 7===

-	Description: Structure of bacteriorhodopsin's M intermediate at pH 7

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Apr 30 08~~:33:28 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19712684}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19712684 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19712684}}
		+
		+	==About this Structure==
		+	2ZZL 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=2ZZL OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19712684</ref><references group="xtra"/>
		+	[[Category: Halobacterium salinarum]]
		+	[[Category: Kouyama, T.]]
		+	[[Category: Yamamoto, M.]]
		+	[[Category: Cell membrane]]
		+	[[Category: Chromophore]]
		+	[[Category: Hydrogen ion transport]]
		+	[[Category: Ion transport]]
		+	[[Category: Membrane]]
		+	[[Category: Photoreceptor protein]]
		+	[[Category: Protein-lipid complex]]
		+	[[Category: Proton transport]]
		+	[[Category: Pyrrolidone carboxylic acid]]
		+	[[Category: Reaction intermediate]]
		+	[[Category: Receptor]]
		+	[[Category: Retinal]]
		+	[[Category: Retinal protein]]
		+	[[Category: Sensory transduction]]
		+	[[Category: Transmembrane]]
		+	[[Category: Transport]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 7 13:58:29 2009''