3gk3 - Revision history

OCA at 09:55, 21 February 2024

2024-02-21T09:55:00Z

←Older revision		Revision as of 09:55, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3gk3' size='340' side='right'caption='[[3gk3]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3gk3' size='340' side='right'caption='[[3gk3]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gk3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Burp1 Burp1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GK3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gk3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GK3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>phbB-2, BURPS1710b_A1014 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~320372 BURP1])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Acetoacetyl-CoA_reductase Acetoacetyl-CoA reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.36 1.1.1.36]~~ </~~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=3gk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gk3 OCA], [https://pdbe.org/3gk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gk3 RCSB], [https://www.ebi.ac.uk/pdbsum/3gk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gk3 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=3gk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gk3 OCA], [https://pdbe.org/3gk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gk3 RCSB], [https://www.ebi.ac.uk/pdbsum/3gk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gk3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q3JJT1_BURP1 Q3JJT1_BURP1]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=3gk3 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=3gk3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. METHODOLOGY/PRINCIPAL FINDINGS: We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. CONCLUSIONS/SIGNIFICANCE: This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.
-
-	Combining functional and structural genomics to sample the essential Burkholderia structome.,Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D 3rd, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC PLoS One. 2013;8(1):e53851. doi: 10.1371/journal.pone.0053851. Epub 2013 Jan 31. PMID:23382856<ref>PMID:23382856</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3gk3" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acetoacetyl-CoA reductase]]~~	+	[[Category: Burkholderia pseudomallei 1710b]]
-	~~[[Category: Burp1~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Structural genomic]]
-	[[Category: Acetoacetyl-co reductase]]
-	[[Category: Oxidoreductase]]
-	[[Category: Ssgcid]]

OCA at 08:07, 9 March 2022

2022-03-09T08:07:10Z

←Older revision		Revision as of 08:07, 9 March 2022
Line 1:		Line 1:

	==Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b==		==Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b==
-	<StructureSection load='3gk3' size='340' side='right' caption='[[3gk3]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3gk3' size='340' side='right'caption='[[3gk3]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gk3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burp1 Burp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GK3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gk3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Burp1 Burp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GK3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phbB-2, BURPS1710b_A1014 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phbB-2, BURPS1710b_A1014 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Acetoacetyl-CoA_reductase Acetoacetyl-CoA reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.36 1.1.1.36] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Acetoacetyl-CoA_reductase Acetoacetyl-CoA reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.36 1.1.1.36] </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=3gk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gk3 OCA], [~~http~~://pdbe.org/3gk3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gk3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gk3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gk3 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=3gk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gk3 OCA], [https://pdbe.org/3gk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gk3 RCSB], [https://www.ebi.ac.uk/pdbsum/3gk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gk3 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	[[Category: Acetoacetyl-CoA reductase]]		[[Category: Acetoacetyl-CoA reductase]]
	[[Category: Burp1]]		[[Category: Burp1]]
		+	[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Acetoacetyl-co reductase]]		[[Category: Acetoacetyl-co reductase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]

OCA at 05:15, 7 December 2018

2018-12-07T05:15:08Z

←Older revision		Revision as of 05:15, 7 December 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gk/3gk3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gk/3gk3_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 21:20, 4 August 2016

2016-08-04T21:20:04Z

←Older revision		Revision as of 21:20, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b==		==Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b==
	<StructureSection load='3gk3' size='340' side='right' caption='[[3gk3]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3gk3' size='340' side='right' caption='[[3gk3]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gk3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GK3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gk3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burp1 Burp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GK3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phbB-2, BURPS1710b_A1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 ~~Burkholderia pseudomallei 1710b~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phbB-2, BURPS1710b_A1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetoacetyl-CoA_reductase Acetoacetyl-CoA reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.36 1.1.1.36] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetoacetyl-CoA_reductase Acetoacetyl-CoA reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.36 1.1.1.36] </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=3gk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gk3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gk3 RCSB], [http://www.ebi.ac.uk/pdbsum/3gk3 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=3gk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gk3 OCA], [http://pdbe.org/3gk3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gk3 RCSB], [http://www.ebi.ac.uk/pdbsum/3gk3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gk3 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	<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=3gk3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 3gk3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Acetoacetyl-CoA reductase]]		[[Category: Acetoacetyl-CoA reductase]]
-	[[Category: ~~Burkholderia pseudomallei 1710b~~]]	+	[[Category: Burp1]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Acetoacetyl-co reductase]]		[[Category: Acetoacetyl-co reductase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]

OCA at 14:50, 18 December 2014

2014-12-18T14:50:19Z

←Older revision		Revision as of 14:50, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3gk3\| PDB=3gk3 \| SCENE= }}~~	+	==Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b==
-	===Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b===	+	<StructureSection load='3gk3' size='340' side='right' caption='[[3gk3]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23382856}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gk3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GK3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">phbB-2, BURPS1710b_A1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 Burkholderia pseudomallei 1710b])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetoacetyl-CoA_reductase Acetoacetyl-CoA reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.36 1.1.1.36] </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=3gk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gk3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gk3 RCSB], [http://www.ebi.ac.uk/pdbsum/3gk3 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/gk/3gk3_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 ==
		+	BACKGROUND: The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. METHODOLOGY/PRINCIPAL FINDINGS: We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. CONCLUSIONS/SIGNIFICANCE: This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.

-	~~==About this Structure==~~	+	Combining functional and structural genomics to sample the essential Burkholderia structome.,Baugh L, Gallagher LA, Patrapuvich R, Clifton MC, Gardberg AS, Edwards TE, Armour B, Begley DW, Dieterich SH, Dranow DM, Abendroth J, Fairman JW, Fox D 3rd, Staker BL, Phan I, Gillespie A, Choi R, Nakazawa-Hewitt S, Nguyen MT, Napuli A, Barrett L, Buchko GW, Stacy R, Myler PJ, Stewart LJ, Manoil C, Van Voorhis WC PLoS One. 2013;8(1):e53851. doi: 10.1371/journal.pone.0053851. Epub 2013 Jan 31. PMID:23382856<ref>PMID:23382856</ref>
-	~~[[3gk3]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3GK3 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023382856</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Acetoacetyl-CoA reductase]]		[[Category: Acetoacetyl-CoA reductase]]
	[[Category: Burkholderia pseudomallei 1710b]]		[[Category: Burkholderia pseudomallei 1710b]]
-	[[Category: ~~SSGCID, Seattle~~ Structural ~~Genomics Center for Infectious Disease.~~]]	+	[[Category: Structural genomic]]
	[[Category: Acetoacetyl-co reductase]]		[[Category: Acetoacetyl-co reductase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Seattle structural genomics center for infectious disease]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
-	[[Category: Structural genomic]]

OCA at 08:17, 30 October 2013

2013-10-30T08:17:41Z

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	{{STRUCTURE_3gk3\| PDB=3gk3 \| SCENE= }}		{{STRUCTURE_3gk3\| PDB=3gk3 \| SCENE= }}
-
	===Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b===		===Crystal structure of acetoacetyl-CoA reductase from Burkholderia pseudomallei 1710b===
-		+	{{ABSTRACT_PUBMED_23382856}}

	==About this Structure==		==About this Structure==
	[[3gk3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA].		[[3gk3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023382856</ref><references group="xtra"/><references/>
	[[Category: Acetoacetyl-CoA reductase]]		[[Category: Acetoacetyl-CoA reductase]]
	[[Category: Burkholderia pseudomallei 1710b]]		[[Category: Burkholderia pseudomallei 1710b]]

OCA: Protected "3gk3" [edit=sysop:move=sysop]

2013-02-27T15:18:35Z

Protected "3gk3" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:18, 27 February 2013

OCA at 15:18, 27 February 2013

2013-02-27T15:18:34Z

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	==About this Structure==		==About this Structure==
-	~~3GK3~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA].	+	[[3gk3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GK3 OCA].
	[[Category: Acetoacetyl-CoA reductase]]		[[Category: Acetoacetyl-CoA reductase]]
	[[Category: Burkholderia pseudomallei 1710b]]		[[Category: Burkholderia pseudomallei 1710b]]
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	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
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OCA at 07:24, 2 December 2009

2009-12-02T07:24:49Z

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