3tml - Revision history

OCA at 13:33, 14 March 2024

OCA — Thu, 14 Mar 2024 13:33:48 GMT

←Older revision		Revision as of 13:33, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3tml' size='340' side='right'caption='[[3tml]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3tml' size='340' side='right'caption='[[3tml]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tml]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Burcj Burcj~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tml]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_cenocepacia_J2315 Burkholderia cenocepacia J2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TML FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3t4c\|3t4c]], [[3sz8\|3sz8]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>kdsA, BceJ2315_21430, BCAL2180 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~216591 BURCJ])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55]~~ </~~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=3tml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tml OCA], [https://pdbe.org/3tml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tml RCSB], [https://www.ebi.ac.uk/pdbsum/3tml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tml 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=3tml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tml OCA], [https://pdbe.org/3tml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tml RCSB], [https://www.ebi.ac.uk/pdbsum/3tml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tml ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/KDSA_BURCJ KDSA_BURCJ]
-	~~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 3tml" style="background-color:#fffaf0;"><~~/~~div>~~	+

	==See Also==		==See Also==
	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]		*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~3-deoxy-8-phosphooctulonate synthase]]~~	+	[[Category: Burkholderia cenocepacia J2315]]
-	~~[[Category: Burcj~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Structural genomic]]
-	[[Category: Ssgcid]]
-	[[Category: Transferase]]

OCA at 17:04, 6 July 2022

OCA — Wed, 06 Jul 2022 17:04:30 GMT

←Older revision		Revision as of 17:04, 6 July 2022
Line 1:		Line 1:

	==Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia==		==Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia==
-	<StructureSection load='3tml' size='340' side='right' caption='[[3tml]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3tml' size='340' side='right'caption='[[3tml]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tml]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Burcj Burcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3TML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tml]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Burcj Burcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TML FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t4c\|3t4c]], [[3sz8\|3sz8]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3t4c\|3t4c]], [[3sz8\|3sz8]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA, BceJ2315_21430, BCAL2180 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 BURCJ])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA, BceJ2315_21430, BCAL2180 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 BURCJ])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=3tml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tml OCA], [~~http~~://pdbe.org/3tml PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3tml RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3tml PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3tml 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=3tml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tml OCA], [https://pdbe.org/3tml PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tml RCSB], [https://www.ebi.ac.uk/pdbsum/3tml PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tml ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Burcj]]		[[Category: Burcj]]
		+	[[Category: Large Structures]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 08:58, 5 August 2016

OCA — Fri, 05 Aug 2016 08:58:22 GMT

←Older revision		Revision as of 08:58, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia==		==Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia==
	<StructureSection load='3tml' size='340' side='right' caption='[[3tml]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3tml' size='340' side='right' caption='[[3tml]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_cenocepacia_j2315 Burkholderia cenocepacia j2315~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TML FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burcj Burcj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TML FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t4c\|3t4c]], [[3sz8\|3sz8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t4c\|3t4c]], [[3sz8\|3sz8]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA, BceJ2315_21430, BCAL2180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 ~~Burkholderia cenocepacia J2315~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA, BceJ2315_21430, BCAL2180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 BURCJ])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=3tml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tml RCSB], [http://www.ebi.ac.uk/pdbsum/3tml 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=3tml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tml OCA], [http://pdbe.org/3tml PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3tml RCSB], [http://www.ebi.ac.uk/pdbsum/3tml PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3tml ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3tml" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
-	[[Category: ~~Burkholderia cenocepacia j2315~~]]	+	[[Category: Burcj]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Ssgcid]]		[[Category: Ssgcid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 07:25, 21 December 2014

OCA — Sun, 21 Dec 2014 07:25:38 GMT

←Older revision		Revision as of 07:25, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3tml\| PDB=3tml \| SCENE= }}~~	+	==Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia==
-	===Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia===	+	<StructureSection load='3tml' size='340' side='right' caption='[[3tml]], [[Resolution\|resolution]] 1.90Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23382856}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia_j2315 Burkholderia cenocepacia j2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3TML FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3t4c\|3t4c]], [[3sz8\|3sz8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">kdsA, BceJ2315_21430, BCAL2180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216591 Burkholderia cenocepacia J2315])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=3tml FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tml OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3tml RCSB], [http://www.ebi.ac.uk/pdbsum/3tml PDBsum]</span></td></tr>
		+	</table>
		+	<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>
-	~~[[3tml]] is a 4 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Burkholderia_cenocepacia_j2315 Burkholderia cenocepacia j2315]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3TML OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
-	*[[Aldolase\|Aldolase]]
	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]		*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:023382856</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Burkholderia cenocepacia j2315]]		[[Category: Burkholderia cenocepacia j2315]]
-	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
-	[[Category: Seattle structural genomics center for infectious disease]]
-	[[Category: Ssgcid]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
		+	[[Category: Ssgcid]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 04:56, 10 October 2013

OCA — Thu, 10 Oct 2013 04:56:44 GMT

←Older revision		Revision as of 04:56, 10 October 2013
Line 1:		Line 1:
-	[[Image:3tml.png\|left\|200px]]
-
	{{STRUCTURE_3tml\| PDB=3tml \| SCENE= }}		{{STRUCTURE_3tml\| PDB=3tml \| SCENE= }}
-
	===Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia===		===Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia===
-		+	{{ABSTRACT_PUBMED_23382856}}

	==About this Structure==		==About this Structure==
-	[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Burkholderia_cenocepacia~~ Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA].	+	[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia_j2315 Burkholderia cenocepacia j2315]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA].

	==See Also==		==See Also==
	*[[Aldolase\|Aldolase]]		*[[Aldolase\|Aldolase]]
		+	*[[Kdo-8-phosphate synthase\|Kdo-8-phosphate synthase]]
		+
		+	==Reference==
		+	<ref group="xtra">PMID:023382856</ref><references group="xtra"/><references/>
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
-	[[Category: Burkholderia cenocepacia]]	+	[[Category: Burkholderia cenocepacia j2315]]
	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]		[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
	[[Category: Seattle structural genomics center for infectious disease]]		[[Category: Seattle structural genomics center for infectious disease]]

OCA at 19:26, 20 October 2012

OCA — Sat, 20 Oct 2012 19:26:49 GMT

←Older revision		Revision as of 19:26, 20 October 2012
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3tml]] is a 4 chain structure ~~of [[Aldolase]]~~ with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA].	+	[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA].

	==See Also==		==See Also==

OCA at 07:22, 27 July 2012

OCA — Fri, 27 Jul 2012 07:22:58 GMT

←Older revision		Revision as of 07:22, 27 July 2012
Line 1:		Line 1:
-	[[Image:3tml.~~jpg~~\|left\|200px]]	+	[[Image:3tml.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3tml", 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_3tml\| PDB=3tml \| SCENE= }}		{{STRUCTURE_3tml\| PDB=3tml \| SCENE= }}

Line 13:		Line 7:

	==About this Structure==		==About this Structure==
-	[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA].	+	[[3tml]] is a 4 chain structure of [[Aldolase]] with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA].
		+
		+	==See Also==
		+	*[[Aldolase\|Aldolase]]
	[[Category: 3-deoxy-8-phosphooctulonate synthase]]		[[Category: 3-deoxy-8-phosphooctulonate synthase]]
	[[Category: Burkholderia cenocepacia]]		[[Category: Burkholderia cenocepacia]]

OCA at 06:14, 21 September 2011

OCA — Wed, 21 Sep 2011 06:14:49 GMT

←Older revision		Revision as of 06:14, 21 September 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3tml.jpg\|left\|200px]]

-	The ~~entry 3tml~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3tml", 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_3tml\| PDB=3tml \| SCENE= }}

-	~~Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)~~	+	===Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia===

-	~~Description: Crystal~~ structure ~~of 2-dehydro~~-3-~~deoxyphosphooctonate aldolase from~~ Burkholderia cenocepacia	+
		+	==About this Structure==
		+	[[3tml]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Burkholderia_cenocepacia Burkholderia cenocepacia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TML OCA].
		+	[[Category: 3-deoxy-8-phosphooctulonate synthase]]
		+	[[Category: Burkholderia cenocepacia]]
		+	[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
		+	[[Category: Seattle structural genomics center for infectious disease]]
		+	[[Category: Ssgcid]]
		+	[[Category: Structural genomic]]
		+	[[Category: Transferase]]

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

OCA — Wed, 07 Sep 2011 05:51:01 GMT

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

←Older revision

Revision as of 05:51, 7 September 2011

OCA: New page: '''Unreleased structure''' The entry 3tml is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of 2-dehydro-3-deoxyphos...

OCA — Wed, 07 Sep 2011 05:51:00 GMT

New page: '''Unreleased structure''' The entry 3tml is ON HOLD Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) Description: Crystal structure of 2-dehydro-3-deoxyphos...

New page

'''Unreleased structure'''

The entry 3tml is ON HOLD

Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Description: Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia cenocepacia