1x1t - Revision history

OCA at 08:04, 25 October 2023

OCA — Wed, 25 Oct 2023 08:04:17 GMT

←Older revision		Revision as of 08:04, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='1x1t' size='340' side='right'caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='1x1t' size='340' side='right'caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_fragi"_eichholz_1902 "bacterium~~ fragi~~" eichholz 1902~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1T FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.52Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1wmb\|1wmb]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/3~~-~~hydroxybutyrate_dehydrogenase 3~~-~~hydroxybutyrate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30]~~ </~~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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [https://pdbe.org/1x1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [https://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1t 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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [https://pdbe.org/1x1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [https://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1t ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5KST5_PSEFR Q5KST5_PSEFR]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacterium fragi eichholz 1902]]
-	[[Category: 3-hydroxybutyrate dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ichihara, E]]	+	[[Category: Pseudomonas fragi]]
-	[[Category: Ito, K]]	+	[[Category: Ichihara E]]
-	[[Category: Nakajima, Y]]	+	[[Category: Ito K]]
-	[[Category: Ogawa, K]]	+	[[Category: Nakajima Y]]
-	[[Category: Yoshimoto, T]]	+	[[Category: Ogawa K]]
-	~~[[Category: Beta-hydroxybutyrate]]~~	+	[[Category: Yoshimoto T]]
-	~~[[Category: Ketone body]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Nadh]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Sdr]]~~	+
-	~~[[Category: Short chain dehydrogenase~~]]	+

OCA at 16:32, 27 October 2021

OCA — Wed, 27 Oct 2021 16:32:36 GMT

←Older revision		Revision as of 16:32, 27 October 2021
Line 3:		Line 3:
	<StructureSection load='1x1t' size='340' side='right'caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='1x1t' size='340' side='right'caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_fragi"_eichholz_1902 "bacterium fragi" eichholz 1902]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1X1T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_fragi"_eichholz_1902 "bacterium fragi" eichholz 1902]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X1T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wmb\|1wmb]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [~~http~~://pdbe.org/1x1t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1t 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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [https://pdbe.org/1x1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [https://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1t ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 17:24, 22 January 2020

OCA — Wed, 22 Jan 2020 17:24:56 GMT

←Older revision		Revision as of 17:24, 22 January 2020
Line 1:		Line 1:

	==Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+==		==Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+==
-	<StructureSection load='1x1t' size='340' side='right' caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>	+	<StructureSection load='1x1t' size='340' side='right'caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fragi"_eichholz_1902 "bacterium fragi" eichholz 1902]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fragi"_eichholz_1902 "bacterium fragi" eichholz 1902]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>
Line 34:		Line 34:
	[[Category: Bacterium fragi eichholz 1902]]		[[Category: Bacterium fragi eichholz 1902]]
	[[Category: 3-hydroxybutyrate dehydrogenase]]		[[Category: 3-hydroxybutyrate dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Ichihara, E]]		[[Category: Ichihara, E]]
	[[Category: Ito, K]]		[[Category: Ito, K]]

OCA at 16:11, 11 April 2018

OCA — Wed, 11 Apr 2018 16:11:01 GMT

←Older revision		Revision as of 16:11, 11 April 2018
Line 1:		Line 1:
		+
	==Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+==		==Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+==
	<StructureSection load='1x1t' size='340' side='right' caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='1x1t' size='340' side='right' caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Atcc_4973 Atcc 4973~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_fragi"_eichholz_1902 "bacterium fragi" eichholz 1902]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://pdbe.org/1x1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [http://www.ebi.ac.uk/pdbsum/1x1t 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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://pdbe.org/1x1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [http://www.ebi.ac.uk/pdbsum/1x1t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1x1t ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x1/1x1t_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x1/1x1t_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=1x1t ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 31:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacterium fragi eichholz 1902]]
	[[Category: 3-hydroxybutyrate dehydrogenase]]		[[Category: 3-hydroxybutyrate dehydrogenase]]
-	[[Category: Atcc 4973]]
	[[Category: Ichihara, E]]		[[Category: Ichihara, E]]
	[[Category: Ito, K]]		[[Category: Ito, K]]

OCA at 21:56, 11 September 2015

OCA — Fri, 11 Sep 2015 21:56:19 GMT

←Older revision		Revision as of 21:56, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1x1t' size='340' side='right' caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='1x1t' size='340' side='right' caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_fragi Pseudomonas fragi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_4973 Atcc 4973]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [http://www.ebi.ac.uk/pdbsum/1x1t 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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://pdbe.org/1x1t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [http://www.ebi.ac.uk/pdbsum/1x1t PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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 1x1t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: 3-hydroxybutyrate dehydrogenase]]		[[Category: 3-hydroxybutyrate dehydrogenase]]
-	[[Category: ~~Pseudomonas fragi~~]]	+	[[Category: Atcc 4973]]
	[[Category: Ichihara, E]]		[[Category: Ichihara, E]]
	[[Category: Ito, K]]		[[Category: Ito, K]]

OCA at 12:34, 6 January 2015

OCA — Tue, 06 Jan 2015 12:34:07 GMT

←Older revision		Revision as of 12:34, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>		<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [http://www.ebi.ac.uk/pdbsum/1x1t 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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [http://www.ebi.ac.uk/pdbsum/1x1t 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 32:		Line 32:
	[[Category: 3-hydroxybutyrate dehydrogenase]]		[[Category: 3-hydroxybutyrate dehydrogenase]]
	[[Category: Pseudomonas fragi]]		[[Category: Pseudomonas fragi]]
-	[[Category: Ichihara, E.]]	+	[[Category: Ichihara, E]]
-	[[Category: Ito, K.]]	+	[[Category: Ito, K]]
-	[[Category: Nakajima, Y.]]	+	[[Category: Nakajima, Y]]
-	[[Category: Ogawa, K.]]	+	[[Category: Ogawa, K]]
-	[[Category: Yoshimoto, T.]]	+	[[Category: Yoshimoto, T]]
	[[Category: Beta-hydroxybutyrate]]		[[Category: Beta-hydroxybutyrate]]
	[[Category: Ketone body]]		[[Category: Ketone body]]

OCA at 19:28, 29 September 2014

OCA — Mon, 29 Sep 2014 19:28:40 GMT

←Older revision		Revision as of 19:28, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1x1t.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+==
		+	<StructureSection load='1x1t' size='340' side='right' caption='[[1x1t]], [[Resolution\|resolution]] 1.52Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1X1T FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wmb\|1wmb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-hydroxybutyrate_dehydrogenase 3-hydroxybutyrate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.30 1.1.1.30] </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=1x1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x1t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1x1t RCSB], [http://www.ebi.ac.uk/pdbsum/1x1t 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/x1/1x1t_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The gene coding for d-3-hydroxybutyrate dehydrogenase (HBDH) was cloned from Pseudomonas fragi. The nucleotide sequence contained a 780 bp open reading frame encoding a 260 amino acid residue protein. The recombinant enzyme was efficiently expressed in Escherichia coli cells harboring pHBDH11 and was purified to homogeneity as judged by SDS-PAGE. The enzyme showed a strict stereospecificity to the D-enantiomer (3R-configuration) of 3-hydroxybutyrate as a substrate. Crystals of the ligand-free HBDH and of the enzyme-NAD+ complex were obtained using the hanging-drop, vapor-diffusion method. The crystal structure of the HBDH was solved by the multiwavelength anomalous diffraction method using the SeMet-substituted enzyme and was refined to 2.0 A resolution. The overall structure of P.fragi HBDH, including the catalytic tetrad of Asn114, Ser142, Tyr155, and Lys159, shows obvious relationships with other members of the short-chain dehydrogenase/reductase (SDR) family. A cacodylate anion was observed in both the ligand-free enzyme and the enzyme-NAD+ complex, and was located near the catalytic tetrad. It was shown that the cacodylate inhibited the NAD+-dependent D-3-hydroxybutyrate dehydrogenation competitively, with a Ki value of 5.6 mM. From the interactions between cacodylate and the enzyme, it is predicted that substrate specificity is achieved through the recognition of the 3-methyl and carboxyl groups of the substrate.

-	~~{{STRUCTURE_1x1t\| PDB=1x1t \| SCENE= }}~~	+	D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme.,Ito K, Nakajima Y, Ichihara E, Ogawa K, Katayama N, Nakashima K, Yoshimoto T J Mol Biol. 2006 Jan 27;355(4):722-33. Epub 2005 Nov 14. PMID:16325199<ref>PMID:16325199</ref>

-	~~===Crystal Structure~~ of ~~D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16325199}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1x1t]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_fragi Pseudomonas fragi]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016325199<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 3-hydroxybutyrate dehydrogenase]]		[[Category: 3-hydroxybutyrate dehydrogenase]]
	[[Category: Pseudomonas fragi]]		[[Category: Pseudomonas fragi]]

OCA: Protected "1x1t" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:35:34 GMT

Protected "1x1t" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:35, 5 January 2013

OCA at 12:35, 5 January 2013

OCA — Sat, 05 Jan 2013 12:35:32 GMT

←Older revision		Revision as of 12:35, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1x1t.png\|left\|200px]]		[[Image:1x1t.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1x1t", 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_1x1t\| PDB=1x1t \| SCENE= }}		{{STRUCTURE_1x1t\| PDB=1x1t \| SCENE= }}

	===Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+===		===Crystal Structure of D-3-Hydroxybutyrate Dehydrogenase from Pseudomonas fragi Complexed with NAD+===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16325199}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16325199 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16325199}}		{{ABSTRACT_PUBMED_16325199}}

	==About this Structure==		==About this Structure==
-	~~1X1T~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA].	+	[[1x1t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16325199~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016325199</ref><references group="xtra"/>
	[[Category: 3-hydroxybutyrate dehydrogenase]]		[[Category: 3-hydroxybutyrate dehydrogenase]]
	[[Category: Pseudomonas fragi]]		[[Category: Pseudomonas fragi]]
Line 35:		Line 23:
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Nadh]]		[[Category: Nadh]]
		+	[[Category: Oxidoreductase]]
	[[Category: Sdr]]		[[Category: Sdr]]
	[[Category: Short chain dehydrogenase]]		[[Category: Short chain dehydrogenase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:38:37 2009''

OCA at 03:38, 18 February 2009

OCA — Wed, 18 Feb 2009 03:38:39 GMT

←Older revision		Revision as of 03:38, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1X1T is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA].	+	1X1T is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X1T OCA].

	==Reference==		==Reference==
-	D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme., Ito K, Nakajima Y, Ichihara E, Ogawa K, Katayama N, Nakashima K, Yoshimoto T, J Mol Biol. 2006 Jan 27;355(4):722-33. Epub 2005 Nov 14. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16325199 16325199]~~	+	<ref group="xtra">PMID:16325199</ref><references group="xtra"/>
	[[Category: 3-hydroxybutyrate dehydrogenase]]		[[Category: 3-hydroxybutyrate dehydrogenase]]
	[[Category: Pseudomonas fragi]]		[[Category: Pseudomonas fragi]]
-	[[Category: Single protein]]
	[[Category: Ichihara, E.]]		[[Category: Ichihara, E.]]
	[[Category: Ito, K.]]		[[Category: Ito, K.]]
Line 39:		Line 38:
	[[Category: Short chain dehydrogenase]]		[[Category: Short chain dehydrogenase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 12~~:21:~~06 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 05:38:37 2009''