2r1l - Revision history

OCA at 09:02, 25 October 2023

2023-10-25T09:02:44Z

←Older revision		Revision as of 09:02, 25 October 2023
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	<StructureSection load='2r1l' size='340' side='right'caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2r1l' size='340' side='right'caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 1.95Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</div></td></tr>	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [https://pdbe.org/2r1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [https://www.ebi.ac.uk/pdbsum/2r1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1l 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=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [https://pdbe.org/2r1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [https://www.ebi.ac.uk/pdbsum/2r1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1l ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q93LD7_RHIRD Q93LD7_RHIRD]
	== 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: ~~Aryldialkylphosphatase~~]]	+	[[Category: Agrobacterium tumefaciens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carr~~, P D~~]]	+	[[Category: Carr PD]]
-	[[Category: Foo~~, J L~~]]	+	[[Category: Foo JL]]
-	[[Category: Jackson~~, C J~~]]	+	[[Category: Jackson CJ]]
-	[[Category: Kim~~, H K~~]]	+	[[Category: Kim HK]]
-	[[Category: Liu~~, J W~~]]	+	[[Category: Liu JW]]
-	[[Category: Ollis~~, D L~~]]	+	[[Category: Ollis DL]]
-	[[Category: Salem, G]]	+	[[Category: Salem G]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Opda]]~~	+
-	~~[[Category: Phosphotriesterase~~]]	+

OCA at 04:11, 2 July 2021

2021-07-02T04:11:30Z

←Older revision		Revision as of 04:11, 2 July 2021
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	==OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A==		==OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A==
-	<StructureSection load='2r1l' size='340' side='right' caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='2r1l' size='340' side='right'caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2R1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [~~http~~://pdbe.org/2r1l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2r1l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1l 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=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [https://pdbe.org/2r1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [https://www.ebi.ac.uk/pdbsum/2r1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1l ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
-	*[[Phosphotriesterase\|Phosphotriesterase]]	+	*[[Phosphotriesterase 3D structures\|Phosphotriesterase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
		+	[[Category: Large Structures]]
	[[Category: Carr, P D]]		[[Category: Carr, P D]]
	[[Category: Foo, J L]]		[[Category: Foo, J L]]

OCA at 11:06, 5 September 2018

2018-09-05T11:06:17Z

←Older revision		Revision as of 11:06, 5 September 2018
Line 1:		Line 1:
		+
	==OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A==		==OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A==
	<StructureSection load='2r1l' size='340' side='right' caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2r1l' size='340' side='right' caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [http://pdbe.org/2r1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [http://www.ebi.ac.uk/pdbsum/2r1l 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=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [http://pdbe.org/2r1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [http://www.ebi.ac.uk/pdbsum/2r1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1l ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/2r1l_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/2r1l_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>
	</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=2r1l ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:36, 11 September 2015

2015-09-11T17:36:59Z

←Older revision		Revision as of 17:36, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2r1l' size='340' side='right' caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='2r1l' size='340' side='right' caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Agrobacterium_tumefaciens Agrobacterium tumefaciens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 ~~Agrobacterium tumefaciens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 "Achromobacter radiobacter" (Beijerinck and van Delden 1902) Bergey et al. 1934])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [http://www.ebi.ac.uk/pdbsum/2r1l 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=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [http://pdbe.org/2r1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [http://www.ebi.ac.uk/pdbsum/2r1l PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2r1l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Agrobacterium tumefaciens]]
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
	[[Category: Carr, P D]]		[[Category: Carr, P D]]

OCA at 15:28, 19 January 2015

2015-01-19T15:28:35Z

←Older revision		Revision as of 15:28, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1L FirstGlance]. <br>		<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1L FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 Agrobacterium tumefaciens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 Agrobacterium tumefaciens])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [http://www.ebi.ac.uk/pdbsum/2r1l 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=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [http://www.ebi.ac.uk/pdbsum/2r1l 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 37:		Line 37:
	[[Category: Agrobacterium tumefaciens]]		[[Category: Agrobacterium tumefaciens]]
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
-	[[Category: Carr, P D.]]	+	[[Category: Carr, P D]]
-	[[Category: Foo, J L.]]	+	[[Category: Foo, J L]]
-	[[Category: Jackson, C J.]]	+	[[Category: Jackson, C J]]
-	[[Category: Kim, H K.]]	+	[[Category: Kim, H K]]
-	[[Category: Liu, J W.]]	+	[[Category: Liu, J W]]
-	[[Category: Ollis, D L.]]	+	[[Category: Ollis, D L]]
-	[[Category: Salem, G.]]	+	[[Category: Salem, G]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Metalloenzyme]]		[[Category: Metalloenzyme]]
	[[Category: Opda]]		[[Category: Opda]]
	[[Category: Phosphotriesterase]]		[[Category: Phosphotriesterase]]

OCA at 07:44, 29 September 2014

2014-09-29T07:44:57Z

←Older revision		Revision as of 07:44, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2r1l.~~png~~\|~~left~~\|200px]]	+	==OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A==
		+	<StructureSection load='2r1l' size='340' side='right' caption='[[2r1l]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2r1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R1L FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2d2j\|2d2j]], [[2d2h\|2d2h]], [[2d2g\|2d2g]], [[2r1k\|2r1k]], [[2r1m\|2r1m]], [[2r1n\|2r1n]], [[2r1o\|2r1o]], [[2r1p\|2r1p]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 Agrobacterium tumefaciens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2r1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2r1l RCSB], [http://www.ebi.ac.uk/pdbsum/2r1l 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/r1/2r1l_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 mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The mu-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems has indicated that mu-hydroxo bridges are often not themselves nucleophiles, but act as general bases for freely exchangeable nucleophilic water molecules. Herein, we present crystallographic analyses of a bacterial PTE from Agrobacterium radiobacter, OpdA, capturing the enzyme-substrate complex during hydrolysis. This model of the Michaelis complex suggests the alignment of the substrate will favour attack from a solvent molecule terminally coordinated to the alpha-metal ion. The bridging of both metal ions by the product, without disruption of the mu-hydroxo bridge, is also consistent with nucleophilic attack occurring from the terminal position. When phosphodiesters are soaked into crystals of OpdA, they coordinate bidentately to the beta-metal ion, displacing the mu-hydroxo bridge. Thus, alternative product-binding modes exist for the PTEs, and it is the bridging mode that appears to result from phosphotriester hydrolysis. Kinetic analysis of the PTE and promiscuous phosphodiesterase activities confirms that the presence of a mu-hydroxo bridge during phosphotriester hydrolysis is correlated with a lower pK(a) for the nucleophile, consistent with a general base function during catalysis.

-	~~{{STRUCTURE_2r1l\| PDB=2r1l \| SCENE= }}~~	+	In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase.,Jackson CJ, Foo JL, Kim HK, Carr PD, Liu JW, Salem G, Ollis DL J Mol Biol. 2008 Feb 1;375(5):1189-96. Epub 2007 Nov 1. PMID:18082180<ref>PMID:18082180</ref>

-	~~===OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with~~ the ~~compound- 1~~.~~95 A===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18082180}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2r1l]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA].~~	+

	==See Also==		==See Also==
	*[[Phosphotriesterase\|Phosphotriesterase]]		*[[Phosphotriesterase\|Phosphotriesterase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018082180<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Agrobacterium tumefaciens]]		[[Category: Agrobacterium tumefaciens]]
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]

OCA at 20:40, 20 October 2012

2012-10-20T20:40:21Z

←Older revision		Revision as of 20:40, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2r1l]] is a 1 chain structure ~~of [[Phosphotriesterase]]~~ with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA].	+	[[2r1l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA].

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

OCA: Protected "2r1l" [edit=sysop:move=sysop]

2012-07-27T11:15:02Z

Protected "2r1l" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:15, 27 July 2012

OCA at 11:15, 27 July 2012

2012-07-27T11:15:00Z

←Older revision		Revision as of 11:15, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2r1l.png\|left\|200px]]		[[Image:2r1l.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2r1l", 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_2r1l\| PDB=2r1l \| SCENE= }}		{{STRUCTURE_2r1l\| PDB=2r1l \| SCENE= }}

	===OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A===		===OpdA from Agrobacterium radiobacter with bound diethyl thiophosphate from crystal soaking with the compound- 1.95 A===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18082180}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18082180 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18082180}}		{{ABSTRACT_PUBMED_18082180}}

	==About this Structure==		==About this Structure==
-	~~2R1L~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA].	+	[[2r1l]] is a 1 chain structure of [[Phosphotriesterase]] with sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA].
		+
		+	==See Also==
		+	*[[Phosphotriesterase\|Phosphotriesterase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18082180~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018082180</ref><references group="xtra"/>
	[[Category: Agrobacterium tumefaciens]]		[[Category: Agrobacterium tumefaciens]]
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
Line 37:		Line 28:
	[[Category: Opda]]		[[Category: Opda]]
	[[Category: Phosphotriesterase]]		[[Category: Phosphotriesterase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:53:14 2009''

OCA at 02:53, 18 February 2009

2009-02-18T02:53:16Z

←Older revision		Revision as of 02:53, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2R1L is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA].	+	2R1L is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1L OCA].

	==Reference==		==Reference==
-	In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase., Jackson CJ, Foo JL, Kim HK, Carr PD, Liu JW, Salem G, Ollis DL, J Mol Biol. 2008 Feb 1;375(5):1189-96. Epub 2007 Nov 1. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18082180 18082180]~~	+	<ref group="xtra">PMID:18082180</ref><references group="xtra"/>
	[[Category: Agrobacterium tumefaciens]]		[[Category: Agrobacterium tumefaciens]]
	[[Category: Aryldialkylphosphatase]]		[[Category: Aryldialkylphosphatase]]
-	[[Category: Single protein]]
	[[Category: Carr, P D.]]		[[Category: Carr, P D.]]
	[[Category: Foo, J L.]]		[[Category: Foo, J L.]]
Line 39:		Line 38:
	[[Category: Phosphotriesterase]]		[[Category: Phosphotriesterase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 11~~:40:~~57 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:53:14 2009''