2gin - Revision history

OCA at 08:49, 25 October 2023

OCA — Wed, 25 Oct 2023 08:49:12 GMT

←Older revision		Revision as of 08:49, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2gin' size='340' side='right'caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2gin' size='340' side='right'caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GIN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>AT3G25770 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~3702 ARATH])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6]~~ </~~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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [https://pdbe.org/2gin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [https://www.ebi.ac.uk/pdbsum/2gin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gin 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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [https://pdbe.org/2gin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [https://www.ebi.ac.uk/pdbsum/2gin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gin ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AOC2_ARATH AOC2_ARATH]] Involved in the production of 12-oxo-phytodienoic acid (OPDA), a precursor of jasmonic acid.	+	[https://www.uniprot.org/uniprot/AOC2_ARATH AOC2_ARATH] Involved in the production of 12-oxo-phytodienoic acid (OPDA), a precursor of jasmonic acid.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Allene-oxide cyclase]]~~	+	[[Category: Arabidopsis thaliana]]
-	~~[[Category: Arath~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hofmann, E]]	+	[[Category: Hofmann E]]
-	[[Category: Schaller, F]]	+	[[Category: Schaller F]]
-	[[Category: Zerbe, P]]	+	[[Category: Zerbe P]]
-	~~[[Category: Beta barrel]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 19:05, 10 March 2021

OCA — Wed, 10 Mar 2021 19:05:44 GMT

←Older revision		Revision as of 19:05, 10 March 2021
Line 1:		Line 1:

	==X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana==		==X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana==
-	<StructureSection load='2gin' size='340' side='right' caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='2gin' size='340' side='right'caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2GIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GIN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT3G25770 ([~~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">AT3G25770 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [~~http~~://pdbe.org/2gin PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2gin PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2gin 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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [https://pdbe.org/2gin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [https://www.ebi.ac.uk/pdbsum/2gin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gin ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AOC2_ARATH AOC2_ARATH]] Involved in the production of 12-oxo-phytodienoic acid (OPDA), a precursor of jasmonic acid.	+	[[https://www.uniprot.org/uniprot/AOC2_ARATH AOC2_ARATH]] Involved in the production of 12-oxo-phytodienoic acid (OPDA), a precursor of jasmonic acid.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: Allene-oxide cyclase]]		[[Category: Allene-oxide cyclase]]
	[[Category: Arath]]		[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Hofmann, E]]		[[Category: Hofmann, E]]
	[[Category: Schaller, F]]		[[Category: Schaller, F]]

OCA at 07:04, 20 June 2018

OCA — Wed, 20 Jun 2018 07:04:52 GMT

←Older revision		Revision as of 07:04, 20 June 2018
Line 1:		Line 1:
		+
	==X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana==		==X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana==
	<StructureSection load='2gin' size='340' side='right' caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2gin' size='340' side='right' caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT3G25770 ([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">AT3G25770 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [http://pdbe.org/2gin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [http://www.ebi.ac.uk/pdbsum/2gin 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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [http://pdbe.org/2gin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [http://www.ebi.ac.uk/pdbsum/2gin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gin ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gi/2gin_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gi/2gin_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 13:22, 9 February 2016

OCA — Tue, 09 Feb 2016 13:22:47 GMT

←Older revision		Revision as of 13:22, 9 February 2016
Line 19:		Line 19:
	<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=2gin ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:38, 10 September 2015

OCA — Thu, 10 Sep 2015 22:38:57 GMT

←Older revision		Revision as of 22:38, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2gin' size='340' side='right' caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='2gin' size='340' side='right' caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GIN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GIN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT3G25770 ([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">AT3G25770 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [http://www.ebi.ac.uk/pdbsum/2gin 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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [http://pdbe.org/2gin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [http://www.ebi.ac.uk/pdbsum/2gin PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2gin" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Allene-oxide cyclase]]		[[Category: Allene-oxide cyclase]]
-	[[Category: ~~Arabidopsis thaliana~~]]	+	[[Category: Arath]]
	[[Category: Hofmann, E]]		[[Category: Hofmann, E]]
	[[Category: Schaller, F]]		[[Category: Schaller, F]]

OCA at 07:04, 25 December 2014

OCA — Thu, 25 Dec 2014 07:04:18 GMT

←Older revision		Revision as of 07:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GIN FirstGlance]. <br>		<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GIN FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT3G25770 ([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">AT3G25770 ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [http://www.ebi.ac.uk/pdbsum/2gin 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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [http://www.ebi.ac.uk/pdbsum/2gin PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AOC2_ARATH AOC2_ARATH]] Involved in the production of 12-oxo-phytodienoic acid (OPDA), a precursor of jasmonic acid.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Allene-oxide cyclase]]		[[Category: Allene-oxide cyclase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
-	[[Category: Hofmann, E.]]	+	[[Category: Hofmann, E]]
-	[[Category: Schaller, F.]]	+	[[Category: Schaller, F]]
-	[[Category: Zerbe, P.]]	+	[[Category: Zerbe, P]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 08:00, 30 September 2014

OCA — Tue, 30 Sep 2014 08:00:54 GMT

←Older revision		Revision as of 08:00, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2gin.~~png~~\|~~left~~\|200px]]	+	==X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana==
		+	<StructureSection load='2gin' size='340' side='right' caption='[[2gin]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2gin]] is a 6 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=2GIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GIN FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2brj\|2brj]], [[1z8k\|1z8k]], [[2dio\|2dio]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AT3G25770 ([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>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allene-oxide_cyclase Allene-oxide cyclase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.99.6 5.3.99.6] </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=2gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gin OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2gin RCSB], [http://www.ebi.ac.uk/pdbsum/2gin 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/gi/2gin_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 ==
		+	We describe the crystallization and structure elucidation of Arabidopsis thaliana allene oxide cyclase 2 (AOC2), a key enzyme in the biosynthesis of jasmonates. In a coupled reaction with allene oxide synthase, AOC2 releases the first cyclic and biologically active metabolite, 12-oxo-phytodienoic acid (OPDA). AOC2 (AT3G25770) folds into an eight-stranded antiparallel beta-barrel with a C-terminal partial helical extension. The protein forms a hydrophobic binding cavity with two distinct polar patches. AOC2 is trimeric in crystals, in vitro and in planta. Based on the observed folding pattern, we assigned AOC2 as a low molecular weight member of the lipocalin family with enzymatic activity in plants. We determined the binding position of the competitive inhibitor vernolic acid (a substrate analog) in the binding pocket. Based on models for bound substrate 12,13-epoxy-9,11,15-octadecatrienoic acid and product OPDA, we propose a reaction scheme that explains the influence of the C15 double bond on reactivity. Reaction is promoted by anchimeric assistance through a conserved Glu residue. The transition state with a pentadienyl carbocation and an oxyanion is stabilized by a strongly bound water molecule and favorable pi-pi interactions with aromatic residues in the cavity. Stereoselectivity results from steric restrictions to the necessary substrate isomerizations imposed by the protein.

-	~~{{STRUCTURE_2gin\| PDB=2gin \| SCENE= }}~~	+	The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction.,Hofmann E, Zerbe P, Schaller F Plant Cell. 2006 Nov;18(11):3201-17. Epub 2006 Nov 3. PMID:17085685<ref>PMID:17085685</ref>

-	~~===X-ray structure~~ of the ~~wt allene oxide cyclase 2 from arabidopsis thaliana===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17085685}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2gin]] is a 6 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=2GIN OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017085685<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Allene-oxide cyclase]]		[[Category: Allene-oxide cyclase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]

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

OCA — Mon, 07 Jan 2013 18:04:45 GMT

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

←Older revision

Revision as of 18:04, 7 January 2013

OCA at 18:04, 7 January 2013

OCA — Mon, 07 Jan 2013 18:04:43 GMT

←Older revision		Revision as of 18:04, 7 January 2013
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-	{{Seed}}
	[[Image:2gin.png\|left\|200px]]		[[Image:2gin.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2gin", 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_2gin\| PDB=2gin \| SCENE= }}		{{STRUCTURE_2gin\| PDB=2gin \| SCENE= }}

	===X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana===		===X-ray structure of the wt allene oxide cyclase 2 from arabidopsis thaliana===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17085685}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17085685 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17085685}}		{{ABSTRACT_PUBMED_17085685}}

	==About this Structure==		==About this Structure==
-	~~2GIN~~ is a 6 ~~chains~~ structure ~~of sequences~~ 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=2GIN OCA].	+	[[2gin]] is a 6 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=2GIN OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17085685~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017085685</ref><references group="xtra"/>
	[[Category: Allene-oxide cyclase]]		[[Category: Allene-oxide cyclase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
Line 30:		Line 18:
	[[Category: Zerbe, P.]]		[[Category: Zerbe, P.]]
	[[Category: Beta barrel]]		[[Category: Beta barrel]]
-		+	[[Category: Isomerase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 10:05:34 2009''~~	+

OCA at 08:05, 17 February 2009

OCA — Tue, 17 Feb 2009 08:05:35 GMT

←Older revision		Revision as of 08:05, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2GIN is a ~~[[Single protein]]~~ structure of ~~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=2GIN OCA].	+	2GIN is a 6 chains structure of sequences 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=2GIN OCA].

	==Reference==		==Reference==
-	The crystal structure of Arabidopsis thaliana allene oxide cyclase: insights into the oxylipin cyclization reaction., Hofmann E, Zerbe P, Schaller F, Plant Cell. 2006 Nov;18(11):3201-17. Epub 2006 Nov 3. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17085685 17085685]~~	+	<ref group="xtra">PMID:17085685</ref><references group="xtra"/>
	[[Category: Allene-oxide cyclase]]		[[Category: Allene-oxide cyclase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
-	[[Category: Single protein]]
	[[Category: Hofmann, E.]]		[[Category: Hofmann, E.]]
	[[Category: Schaller, F.]]		[[Category: Schaller, F.]]
Line 32:		Line 31:
	[[Category: Beta barrel]]		[[Category: Beta barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 13~~:51:~~01 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:05:34 2009''