2q4e - Revision history

OCA at 08:31, 30 October 2024

2024-10-30T08:31:47Z

← Older revision		Revision as of 08:31, 30 October 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>
	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.49Å</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]] 2.49Å, 16 models</td></tr>
	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [https://pdbe.org/2q4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [https://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e 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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [https://pdbe.org/2q4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [https://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e ProSAT]</span></td></tr>
Line 15:		Line 15:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4e_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4e_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>

OCA at 11:19, 30 August 2023

2023-08-30T11:19:10Z

← Older revision		Revision as of 11:19, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2q4e' size='340' side='right'caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='2q4e' size='340' side='right'caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>
	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 2.49Å</td></tr>
	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1ydw\|1ydw]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~At4g09670, F17A8.20 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])~~</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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [https://pdbe.org/2q4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [https://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e 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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [https://pdbe.org/2q4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [https://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Y4967_ARATH Y4967_ARATH]
	== 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: ~~Arath~~]]		[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: Structural genomic]]~~		[[Category: Kondrashov DA]]
	[[Category: Kondrashov~~, D A~~]]		[[Category: Levin EJ]]
	[[Category: Levin~~, E J~~]]		[[Category: Phillips Jr GN]]
	[[Category: Phillips~~, G N~~]]		[[Category: Wesenberg GE]]
	[[Category: Wesenberg~~, G E]]~~
	~~[[Category: At4g09670]]~~
	~~[[Category: Cesg]]~~
	~~[[Category: Ensemble refinement]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: PSI, Protein structure initiative]]~~
	~~[[Category: Refinement methodology development~~]]

OCA at 08:07, 25 June 2021

2021-06-25T08:07:46Z

← Older revision		Revision as of 08:07, 25 June 2021
Line 1:		Line 1:
	~~{{Large structure}}~~
	==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670==		==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670==
	<StructureSection load='2q4e' size='340' side='right' caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='2q4e' size='340' side='right'caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ydw\|1ydw]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [~~http~~://pdbe.org/2q4e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e 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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [https://pdbe.org/2q4e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [https://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e ProSAT]</span></td></tr>
	</table>		</table>
	~~{{Large structure}}~~
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
			[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Kondrashov, D A]]		[[Category: Kondrashov, D A]]

OCA at 08:21, 29 August 2018

2018-08-29T08:21:25Z

← Older revision		Revision as of 08:21, 29 August 2018
Line 1:		Line 1:
			{{Large structure}}
	==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670==		==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670==
	<StructureSection load='2q4e' size='340' side='right' caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='2q4e' size='340' side='right' caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://pdbe.org/2q4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [http://www.ebi.ac.uk/pdbsum/2q4e 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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://pdbe.org/2q4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [http://www.ebi.ac.uk/pdbsum/2q4e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4e ProSAT]</span></td></tr>
	</table>		</table>
	{{Large structure}}		{{Large structure}}
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4e_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4e_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 10:49, 8 February 2016

2016-02-08T10:49:40Z

← Older revision		Revision as of 10:49, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q4e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:49, 10 September 2015

2015-09-10T10:49:15Z

← Older revision		Revision as of 10:49, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2q4e' size='340' side='right' caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='2q4e' size='340' side='right' caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arabidopsis_thaliana Arabidopsis thaliana~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ~~Arabidopsis thaliana~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [http://www.ebi.ac.uk/pdbsum/2q4e 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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://pdbe.org/2q4e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [http://www.ebi.ac.uk/pdbsum/2q4e PDBsum]</span></td></tr>
	</table>		</table>
			{{Large structure}}
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		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 2q4e" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Arabidopsis thaliana~~]]		[[Category: Arath]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Kondrashov, D A]]		[[Category: Kondrashov, D A]]

OCA at 14:57, 19 January 2015

2015-01-19T14:57:55Z

← Older revision		Revision as of 14:57, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [http://www.ebi.ac.uk/pdbsum/2q4e 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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [http://www.ebi.ac.uk/pdbsum/2q4e PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: ~~CESG, Center for Eukaryotic~~ Structural ~~Genomics.~~]]		[[Category: Structural genomic]]
	[[Category: Kondrashov, D A.]]		[[Category: Kondrashov, D A]]
	[[Category: Levin, E J.]]		[[Category: Levin, E J]]
	[[Category: Phillips, G N.]]		[[Category: Phillips, G N]]
	[[Category: Wesenberg, G E.]]		[[Category: Wesenberg, G E]]
	[[Category: At4g09670]]		[[Category: At4g09670]]
	~~[[Category: Center for eukaryotic structural genomic]]~~
	[[Category: Cesg]]		[[Category: Cesg]]
	[[Category: Ensemble refinement]]		[[Category: Ensemble refinement]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Protein structure initiative]]		[[Category: PSI, Protein structure initiative]]
	~~[[Category: Psi~~]]
	[[Category: Refinement methodology development]]		[[Category: Refinement methodology development]]
	~~[[Category: Structural genomic]]~~

OCA at 18:38, 30 September 2014

2014-09-30T18:38:27Z

← Older revision		Revision as of 18:38, 30 September 2014
Line 1:		Line 1:
	~~{{Large structure}}~~		==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670==
	~~{{STRUCTURE_2q4e\| PDB=2q4e \| SCENE= }}~~		<StructureSection load='2q4e' size='340' side='right' caption='[[2q4e]], [[Resolution\|resolution]] 2.49Å' scene=''>
	===Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670===		== Structural highlights ==
	~~{{ABSTRACT_PUBMED_17850744}}~~		<table><tr><td colspan='2'>[[2q4e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q4E FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ydw\|1ydw]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">At4g09670, F17A8.20 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=2q4e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q4e RCSB], [http://www.ebi.ac.uk/pdbsum/2q4e 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/q4/2q4e_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 ==
			X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

	~~==About this Structure==~~		Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</ref>
	~~[[2q4e]] is a 2 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4E OCA].~~

	==~~Reference~~==		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	<~~ref group="xtra">PMID:017850744<~~/~~ref~~><~~references group="xtra"~~/>		</div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: CESG, Center for Eukaryotic Structural Genomics.]]		[[Category: CESG, Center for Eukaryotic Structural Genomics.]]

OCA at 07:45, 11 March 2013

2013-03-11T07:45:51Z

@@ Line 1: / Line 1: @@
-[[Image:2q4e.png|left|200px]]
+{{Large structure}}
 {{STRUCTURE_2q4e|  PDB=2q4e  |  SCENE=  }}
 ===Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At4g09670===
 {{ABSTRACT_PUBMED_17850744}}

OCA: Protected "2q4e" [edit=sysop:move=sysop]

2011-08-10T04:55:42Z

Protected "2q4e" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:55, 10 August 2011
(No difference)