2rdb - Revision history

OCA at 11:54, 30 August 2023

OCA — Wed, 30 Aug 2023 11:54:24 GMT

←Older revision		Revision as of 11:54, 30 August 2023
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	<StructureSection load='2rdb' size='340' side='right'caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2rdb' size='340' side='right'caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</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]] 2.1Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923])</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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [https://pdbe.org/2rdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [https://www.ebi.ac.uk/pdbsum/2rdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdb 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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [https://pdbe.org/2rdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [https://www.ebi.ac.uk/pdbsum/2rdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O87798_STUST O87798_STUST]
	== 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: Achromobacter sewerinii bergey et al. 1923]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davydov, R]]	+	[[Category: Pseudomonas stutzeri]]
-	[[Category: Garcia-Serres, R]]	+	[[Category: Davydov R]]
-	[[Category: Hoffman~~, B M~~]]	+	[[Category: Garcia-Serres R]]
-	[[Category: Huynh~~, B H~~]]	+	[[Category: Hoffman BM]]
-	[[Category: Lippard~~, S J~~]]	+	[[Category: Huynh BH]]
-	[[Category: McCormick~~, M S~~]]	+	[[Category: Lippard SJ]]
-	[[Category: Murray~~, L J~~]]	+	[[Category: McCormick MS]]
-	[[Category: Naik, S]]	+	[[Category: Murray LJ]]
-	~~[[Category: 4-helix bundle]]~~	+	[[Category: Naik S]]
-	~~[[Category: Carboxylate bridge]]~~	+
-	~~[[Category: Diiron]]~~	+
-	~~[[Category: Metalloenzyme]]~~	+
-	~~[[Category: Monooxygenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Tryptophan radical~~]]	+

OCA at 04:22, 2 July 2021

OCA — Fri, 02 Jul 2021 04:22:09 GMT

←Older revision		Revision as of 04:22, 2 July 2021
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	==X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant==		==X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant==
-	<StructureSection load='2rdb' size='340' side='right' caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2rdb' size='340' side='right'caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touE ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923])</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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [~~http~~://pdbe.org/2rdb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rdb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdb 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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [https://pdbe.org/2rdb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [https://www.ebi.ac.uk/pdbsum/2rdb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rd/2rdb_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 2rdb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2rdb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Achromobacter sewerinii bergey et al. 1923]]		[[Category: Achromobacter sewerinii bergey et al. 1923]]
		+	[[Category: Large Structures]]
	[[Category: Davydov, R]]		[[Category: Davydov, R]]
	[[Category: Garcia-Serres, R]]		[[Category: Garcia-Serres, R]]

OCA at 07:49, 25 October 2017

OCA — Wed, 25 Oct 2017 07:49:11 GMT

←Older revision		Revision as of 07:49, 25 October 2017
Line 1:		Line 1:
		+
	==X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant==		==X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant==
	<StructureSection load='2rdb' size='340' side='right' caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2rdb' size='340' side='right' caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923])</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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://pdbe.org/2rdb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb 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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://pdbe.org/2rdb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdb ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 17:26, 8 February 2016

OCA — Mon, 08 Feb 2016 17:26:35 GMT

←Older revision		Revision as of 17:26, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2rdb' size='340' side='right' caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2rdb' size='340' side='right' caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_stutzeri Pseudomonas stutzeri~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_sewerinii"_bergey_et_al._1923 "achromobacter sewerinii" bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 ~~Pseudomonas stutzeri~~]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 ~~Pseudomonas stutzeri~~]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 ~~Pseudomonas stutzeri~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 "Achromobacter sewerinii" Bergey et al. 1923])</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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb 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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://pdbe.org/2rdb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<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=2rdb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 2rdb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pseudomonas stutzeri~~]]	+	[[Category: Achromobacter sewerinii bergey et al. 1923]]
	[[Category: Davydov, R]]		[[Category: Davydov, R]]
	[[Category: Garcia-Serres, R]]		[[Category: Garcia-Serres, R]]

OCA at 14:20, 19 January 2015

OCA — Mon, 19 Jan 2015 14:20:22 GMT

←Older revision		Revision as of 14:20, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri])</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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb 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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb 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: Pseudomonas stutzeri]]		[[Category: Pseudomonas stutzeri]]
-	[[Category: Davydov, R.]]	+	[[Category: Davydov, R]]
-	[[Category: Garcia-Serres, R.]]	+	[[Category: Garcia-Serres, R]]
-	[[Category: Hoffman, B M.]]	+	[[Category: Hoffman, B M]]
-	[[Category: Huynh, B H.]]	+	[[Category: Huynh, B H]]
-	[[Category: Lippard, S J.]]	+	[[Category: Lippard, S J]]
-	[[Category: McCormick, M S.]]	+	[[Category: McCormick, M S]]
-	[[Category: Murray, L J.]]	+	[[Category: Murray, L J]]
-	[[Category: Naik, S.]]	+	[[Category: Naik, S]]
	[[Category: 4-helix bundle]]		[[Category: 4-helix bundle]]
	[[Category: Carboxylate bridge]]		[[Category: Carboxylate bridge]]

OCA at 18:27, 30 September 2014

OCA — Tue, 30 Sep 2014 18:27:06 GMT

←Older revision		Revision as of 18:27, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2rdb.~~png~~\|~~left~~\|200px]]	+	==X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant==
		+	<StructureSection load='2rdb' size='340' side='right' caption='[[2rdb]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rdb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RDB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2inc\|2inc]], [[2ind\|2ind]], [[1t0q\|1t0q]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">touA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri]), touE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri]), touB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316 Pseudomonas stutzeri])</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=2rdb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rdb RCSB], [http://www.ebi.ac.uk/pdbsum/2rdb 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/rd/2rdb_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 ==
		+	At its carboxylate-bridged diiron active site, the hydroxylase component of toluene/o-xylene monooxygenase activates dioxygen for subsequent arene hydroxylation. In an I100W variant of this enzyme, we characterized the formation and decay of two species formed by addition of dioxygen to the reduced, diiron(II) state by rapid-freeze quench (RFQ) EPR, Mossbauer, and ENDOR spectroscopy. The dependence of the formation and decay rates of this mixed-valent transient on pH and the presence of phenol, propylene, or acetylene was investigated by double-mixing stopped-flow optical spectroscopy. Modification of the alpha-subunit of the hydroxylase after reaction of the reduced protein with dioxygen-saturated buffer was investigated by tryptic digestion coupled mass spectrometry. From these investigations, we conclude that (i) a diiron(III,IV)-W* transient, kinetically linked to a preceding diiron(III) intermediate, arises from the one-electron oxidation of W100, (ii) the tryptophan radical is deprotonated, (iii) rapid exchange of either a terminal water or hydroxide ion with water occurs at the ferric ion in the diiron(III,IV) cluster, and (iv) the diiron(III,IV) core and W* decay to the diiron(III) product by a common mechanism. No transient radical was observed by stopped-flow optical spectroscopy for reactions of the reduced hydroxylase variants I100Y, L208F, and F205W with dioxygen. The absence of such species, and the deprotonated state of the tryptophanyl radical in the diiron(III,IV)-W* transient, allow for a conservative estimate of the reduction potential of the diiron(III) intermediate as lying between 1.1 and 1.3 V. We also describe the X-ray crystal structure of the I100W variant of ToMOH.

-	~~{{STRUCTURE_2rdb\| PDB=2rdb \| SCENE= }}~~	+	Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase.,Murray LJ, Garcia-Serres R, McCormick MS, Davydov R, Naik SG, Kim SH, Hoffman BM, Huynh BH, Lippard SJ Biochemistry. 2007 Dec 25;46(51):14795-809. Epub 2007 Nov 29. PMID:18044971<ref>PMID:18044971</ref>

-	~~===X-ray Crystal Structure of Toluene~~/~~o-Xylene Monooxygenase Hydroxylase I100W Mutant===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18044971}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2rdb]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018044971<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pseudomonas stutzeri]]		[[Category: Pseudomonas stutzeri]]
	[[Category: Davydov, R.]]		[[Category: Davydov, R.]]

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

OCA — Mon, 07 Jan 2013 21:05:04 GMT

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

←Older revision

Revision as of 21:05, 7 January 2013

OCA at 21:05, 7 January 2013

OCA — Mon, 07 Jan 2013 21:05:01 GMT

←Older revision		Revision as of 21:05, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2rdb.png\|left\|200px]]		[[Image:2rdb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rdb", 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_2rdb\| PDB=2rdb \| SCENE= }}		{{STRUCTURE_2rdb\| PDB=2rdb \| SCENE= }}

	===X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant===		===X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18044971}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18044971 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18044971}}		{{ABSTRACT_PUBMED_18044971}}

	==About this Structure==		==About this Structure==
-	~~2RDB~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA].	+	[[2rdb]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18044971~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018044971</ref><references group="xtra"/>
	[[Category: Pseudomonas stutzeri]]		[[Category: Pseudomonas stutzeri]]
	[[Category: Davydov, R.]]		[[Category: Davydov, R.]]
Line 40:		Line 28:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Tryptophan radical]]		[[Category: Tryptophan radical]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:46:37 2009''

OCA at 22:46, 16 February 2009

OCA — Mon, 16 Feb 2009 22:46:39 GMT

←Older revision		Revision as of 22:46, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2RDB is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA].	+	2RDB is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_stutzeri Pseudomonas stutzeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDB OCA].

	==Reference==		==Reference==
-	Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase., Murray LJ, Garcia-Serres R, McCormick MS, Davydov R, Naik SG, Kim SH, Hoffman BM, Huynh BH, Lippard SJ, Biochemistry. 2007 Dec 25;46(51):14795-809. Epub 2007 Nov 29. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18044971 18044971]~~	+	<ref group="xtra">PMID:18044971</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Pseudomonas stutzeri]]		[[Category: Pseudomonas stutzeri]]
	[[Category: Davydov, R.]]		[[Category: Davydov, R.]]
Line 42:		Line 41:
	[[Category: Tryptophan radical]]		[[Category: Tryptophan radical]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 05~~:16:~~29 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:46:37 2009''

OCA at 02:16, 28 July 2008

OCA — Mon, 28 Jul 2008 02:16:30 GMT

←Older revision		Revision as of 02:16, 28 July 2008
Line 1:		Line 1:
-	[[Image:2rdb.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2rdb.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2rdb\| PDB=2rdb \| SCENE= }}		{{STRUCTURE_2rdb\| PDB=2rdb \| SCENE= }}

-	~~'''~~X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant~~'''~~	+	===X-ray Crystal Structure of Toluene/o-Xylene Monooxygenase Hydroxylase I100W Mutant===


-	~~==Overview==~~	+	<!--
-	~~At its carboxylate~~-~~bridged diiron active site, the hydroxylase component of toluene/o~~-~~xylene monooxygenase activates dioxygen for subsequent arene hydroxylation. In an I100W variant of~~ this ~~enzyme~~, ~~we characterized~~ the ~~formation and decay of two species formed by addition of dioxygen~~ to the ~~reduced, diiron~~(~~II) state by rapid-freeze quench (RFQ) EPR, Mossbauer, and ENDOR spectroscopy. The dependence of the formation and decay rates of this mixed-valent transient~~ on ~~pH and the presence of phenol, propylene, or acetylene was investigated by double-mixing stopped-flow optical spectroscopy~~. ~~Modification of the alpha-subunit of the hydroxylase after reaction of the reduced protein with dioxygen-saturated buffer was investigated by tryptic digestion coupled mass spectrometry~~. ~~From these investigations, we conclude that (i~~) ~~a diiron(III~~,~~IV)-W* transient, kinetically linked to a preceding diiron(III) intermediate, arises from the one-electron oxidation of W100, (ii) the tryptophan radical~~ is ~~deprotonated, (iii) rapid exchange of either a terminal water or hydroxide ion with water occurs at~~ the ~~ferric ion in the diiron(III,IV) cluster, and (iv) the diiron(III,IV) core and W* decay to the diiron(III) product by a common mechanism~~. ~~No transient radical was observed by stopped~~-flow optical spectroscopy for reactions of the reduced hydroxylase variants I100Y, L208F, and F205W with dioxygen. The absence of such species, and the deprotonated state of the tryptophanyl radical in the diiron(III,IV)-W* transient, allow for a conservative estimate of the reduction potential of the diiron(III) intermediate as lying between 1.1 and 1.3 V. We also describe the X-ray crystal structure of the I100W variant of ToMOH.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18044971}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18044971 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18044971}}

	==About this Structure==		==About this Structure==
Line 37:		Line 41:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Tryptophan radical]]		[[Category: Tryptophan radical]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Apr 16 23~~:07:43 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 05:16:29 2008''