2q3u - Revision history

OCA at 11:17, 30 August 2023

OCA — Wed, 30 Aug 2023 11:17:38 GMT

←Older revision		Revision as of 11:17, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='2q3u' size='340' side='right'caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='2q3u' size='340' side='right'caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3U FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3~~[~~N-MORPHOLINO~~]~~PROPANE+SULFONIC+ACID'>MPO</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]] 1.53Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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;'>[[1vkp\|1vkp~~]~~]</div></td></tr>~~	+
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">AIH~~, ~~At5g08170, T22D6.110 ([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/Agmatine_deiminase Agmatine deiminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12]~~ </~~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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [https://pdbe.org/2q3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [https://www.ebi.ac.uk/pdbsum/2q3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3u 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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [https://pdbe.org/2q3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [https://www.ebi.ac.uk/pdbsum/2q3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AGUA_ARATH AGUA_ARATH]] Mediates the hydrolysis of agmatine into N-carbamoylputrescine in the arginine decarboxylase (ADC) pathway of putrescine biosynthesis, a basic polyamine.	+	[https://www.uniprot.org/uniprot/AGUA_ARATH AGUA_ARATH] Mediates the hydrolysis of agmatine into N-carbamoylputrescine in the arginine decarboxylase (ADC) pathway of putrescine biosynthesis, a basic polyamine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Agmatine deiminase]]~~	+	[[Category: Arabidopsis thaliana]]
-	~~[[Category: Arath~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Structural genomic]]~~	+	[[Category: Kondrashov DA]]
-	[[Category: Kondrashov~~, D A~~]]	+	[[Category: Levin EJ]]
-	[[Category: Levin~~, E J~~]]	+	[[Category: Phillips Jr GN]]
-	[[Category: Phillips~~, G N~~]]	+	[[Category: Wesenberg GE]]
-	[[Category: Wesenberg~~, G E]]~~	+
-	~~[[Category: Agmatine iminohydrolase]]~~	+
-	~~[[Category: Aih]]~~	+
-	~~[[Category: At5g08170]]~~	+
-	~~[[Category: Cesg]]~~	+
-	~~[[Category: Ensemble refinement]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: N-carbamoylputrescine]]~~	+
-	~~[[Category: Polyamine biosynthesis]]~~	+
-	~~[[Category: PSI, Protein structure initiative]]~~	+
-	~~[[Category: Putrescine]]~~	+
-	~~[[Category: Refinement methodology development~~]]	+

OCA at 08:07, 25 June 2021

OCA — Fri, 25 Jun 2021 08:07:02 GMT

OCA at 08:18, 29 August 2018

OCA — Wed, 29 Aug 2018 08:18:59 GMT

←Older revision		Revision as of 08:18, 29 August 2018
Line 1:		Line 1:
		+
	==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase==		==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase==
	<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>
Line 8:		Line 9:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIH, At5g08170, T22D6.110 ([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">AIH, At5g08170, T22D6.110 ([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/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://pdbe.org/2q3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u 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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://pdbe.org/2q3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/2q3u_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q3/2q3u_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=2q3u ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:01, 11 September 2015

OCA — Fri, 11 Sep 2015 15:01:34 GMT

←Older revision		Revision as of 15:01, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arabidopsis_thaliana Arabidopsis thaliana~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q3U FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vkp\|1vkp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vkp\|1vkp]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIH, At5g08170, T22D6.110 ([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">AIH, At5g08170, T22D6.110 ([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/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u 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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://pdbe.org/2q3u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2q3u" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
-	[[Category: ~~Arabidopsis thaliana~~]]	+	[[Category: Arath]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Kondrashov, D A]]		[[Category: Kondrashov, D A]]

OCA at 18:05, 25 December 2014

OCA — Thu, 25 Dec 2014 18:05:32 GMT

←Older revision		Revision as of 18:05, 25 December 2014
Line 10:		Line 10:
	<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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u 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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AGUA_ARATH AGUA_ARATH]] Mediates the hydrolysis of agmatine into N-carbamoylputrescine in the arginine decarboxylase (ADC) pathway of putrescine biosynthesis, a basic polyamine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
-	[[Category: ~~CESG, Center for Eukaryotic~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Kondrashov, D A.]]	+	[[Category: Kondrashov, D A]]
-	[[Category: Levin, E J.]]	+	[[Category: Levin, E J]]
-	[[Category: Phillips, G N.]]	+	[[Category: Phillips, G N]]
-	[[Category: Wesenberg, G E~~.]]~~	+	[[Category: Wesenberg, G E]]
-	~~[[Category: Agmatine deiminase~~]]	+
	[[Category: Agmatine iminohydrolase]]		[[Category: Agmatine iminohydrolase]]
	[[Category: Aih]]		[[Category: Aih]]
	[[Category: At5g08170]]		[[Category: At5g08170]]
-	[[Category: Center for eukaryotic structural genomic]]
	[[Category: Cesg]]		[[Category: Cesg]]
	[[Category: Ensemble refinement]]		[[Category: Ensemble refinement]]
Line 49:		Line 49:
	[[Category: N-carbamoylputrescine]]		[[Category: N-carbamoylputrescine]]
	[[Category: Polyamine biosynthesis]]		[[Category: Polyamine biosynthesis]]
-	[[Category: Protein structure initiative]]	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category: Psi~~]]	+
	[[Category: Putrescine]]		[[Category: Putrescine]]
	[[Category: Refinement methodology development]]		[[Category: Refinement methodology development]]
-	[[Category: Structural genomic]]

OCA at 05:49, 10 October 2014

OCA — Fri, 10 Oct 2014 05:49:09 GMT

←Older revision		Revision as of 05:49, 10 October 2014
Line 2:		Line 2:
	<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. <br>	+	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q3U FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vkp\|1vkp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vkp\|1vkp]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIH, At5g08170, T22D6.110 ([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">AIH, At5g08170, T22D6.110 ([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/~~Glucokinase Glucokinase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.~~2 2~~.7.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u 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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u 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 26:		Line 26:
	Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</ref>		Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==

OCA at 08:33, 7 May 2014

OCA — Wed, 07 May 2014 08:33:38 GMT

←Older revision		Revision as of 08:33, 7 May 2014
Line 1:		Line 1:
-	[[~~Image:~~2q3u.~~png~~\|~~left~~\|200px]]	+	==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase==
		+	<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vkp\|1vkp]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIH, At5g08170, T22D6.110 ([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/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [http://www.ebi.ac.uk/pdbsum/2q3u 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/q3/2q3u_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

-	~~<!--~~	+	Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2q3u"~~, ~~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_2q3u\| PDB=2q3u \| SCENE= }}~~	+

-	~~===Ensemble refinement~~ of the ~~protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_17850744}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 17850744 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_17850744}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2q3u]] is a 2 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017850744<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]

OCA: Protected "2q3u" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2011 04:52:13 GMT

Protected "2q3u" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 10 August 2011

OCA at 04:52, 10 August 2011

OCA — Wed, 10 Aug 2011 04:52:11 GMT

←Older revision		Revision as of 04:52, 10 August 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2q3u.png\|left\|200px]]		[[Image:2q3u.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2Q3U~~ is a 2 ~~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=2Q3U OCA].	+	[[2q3u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17850744~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017850744</ref><references group="xtra"/>
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: CESG, Center for Eukaryotic Structural Genomics.]]		[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
-	[[Category: Jr., G N.Phillips.]]
	[[Category: Kondrashov, D A.]]		[[Category: Kondrashov, D A.]]
	[[Category: Levin, E J.]]		[[Category: Levin, E J.]]
		+	[[Category: Phillips, G N.]]
	[[Category: Wesenberg, G E.]]		[[Category: Wesenberg, G E.]]
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
Line 38:		Line 37:
	[[Category: Cesg]]		[[Category: Cesg]]
	[[Category: Ensemble refinement]]		[[Category: Ensemble refinement]]
		+	[[Category: Hydrolase]]
	[[Category: N-carbamoylputrescine]]		[[Category: N-carbamoylputrescine]]
	[[Category: Polyamine biosynthesis]]		[[Category: Polyamine biosynthesis]]
Line 45:		Line 45:
	[[Category: Refinement methodology development]]		[[Category: Refinement methodology development]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:02:50 2009''

OCA at 23:02, 17 February 2009

OCA — Tue, 17 Feb 2009 23:02:56 GMT

←Older revision		Revision as of 23:02, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Q3U 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=2Q3U OCA].	+	2Q3U is a 2 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=2Q3U OCA].

	==Reference==		==Reference==
-	~~Ensemble refinement of protein crystal structures: validation and application., Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr, Structure. 2007 Sep;15(9):1040-52.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17850744 17850744]~~	+	<ref group="xtra">PMID:17850744</ref><references group="xtra"/>
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
-	[[Category: Single protein]]
	[[Category: CESG, Center for Eukaryotic Structural Genomics.]]		[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
	[[Category: Jr., G N.Phillips.]]		[[Category: Jr., G N.Phillips.]]
Line 47:		Line 46:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Jul 10 12~~:37:~~26 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:02:50 2009''

←Older revision		Revision as of 08:07, 25 June 2021
Line 1:		Line 1:

	==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase==		==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase==
-	<StructureSection load='2q3u' size='340' side='right' caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>	+	<StructureSection load='2q3u' size='340' side='right'caption='[[2q3u]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Q3U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2q3u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPO:3[N-MORPHOLINO]PROPANE+SULFONIC+ACID'>MPO</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1vkp\|1vkp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1vkp\|1vkp]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIH, At5g08170, T22D6.110 ([~~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">AIH, At5g08170, T22D6.110 ([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/Agmatine_deiminase Agmatine deiminase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Agmatine_deiminase Agmatine deiminase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.12 3.5.3.12] </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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [~~http~~://pdbe.org/2q3u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2q3u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3u 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=2q3u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3u OCA], [https://pdbe.org/2q3u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3u RCSB], [https://www.ebi.ac.uk/pdbsum/2q3u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3u ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AGUA_ARATH AGUA_ARATH]] Mediates the hydrolysis of agmatine into N-carbamoylputrescine in the arginine decarboxylase (ADC) pathway of putrescine biosynthesis, a basic polyamine.	+	[[https://www.uniprot.org/uniprot/AGUA_ARATH AGUA_ARATH]] Mediates the hydrolysis of agmatine into N-carbamoylputrescine in the arginine decarboxylase (ADC) pathway of putrescine biosynthesis, a basic polyamine.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 38:
	[[Category: Agmatine deiminase]]		[[Category: Agmatine deiminase]]
	[[Category: Arath]]		[[Category: Arath]]
		+	[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Kondrashov, D A]]		[[Category: Kondrashov, D A]]