3UND

Substrate-bound crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Combining functional and structural genomics to sample the essential Burkholderia structome.

Baugh, L.Gallagher, L.A.Patrapuvich, R.Clifton, M.C.Gardberg, A.S.Edwards, T.E.Armour, B.Begley, D.W.Dieterich, S.H.Dranow, D.M.Abendroth, J.Fairman, J.W.Fox, D.Staker, B.L.Phan, I.Gillespie, A.Choi, R.Nakazawa-Hewitt, S.Nguyen, M.T.Napuli, A.Barrett, L.Buchko, G.W.Stacy, R.Myler, P.J.Stewart, L.J.Manoil, C.Van Voorhis, W.C.

(2013) PLoS One 8: e53851-e53851

  • DOI: https://doi.org/10.1371/journal.pone.0053851
  • Primary Citation of Related Structures:  
    3D63, 3DAH, 3EIZ, 3EJ2, 3EK2, 3EZO, 3F0F, 3FTP, 3GK0, 3GK3, 3GVF, 3GWA, 3GWE, 3IML, 3SZ8, 3T4C, 3TML, 3TMQ, 3TXY, 3U7J, 3UE9, 3UK1, 3UK2, 3UND, 3UPT, 3URR, 3UW1, 3UW2, 3UW3, 3V2I, 3V7N, 3V8H, 3V9O, 3V9P, 3VAV, 4DDO, 4DFE, 4DHE, 4DHK, 4DUT, 4DZ4, 4E4T, 4EFI, 4EG0, 4EGJ, 4EK2, 4EQY, 4EWG, 4EXQ, 4F2G

  • PubMed Abstract: 

    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. 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. 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.


  • Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease, Seattle, Washington, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-dehydro-3-deoxyphosphooctonate aldolase 2
A, B, C, D
285Burkholderia pseudomallei 1710bMutation(s): 0 
Gene Names: kdsAkdsA2BURPS1710b_3264
EC: 2.5.1.55
UniProt
Find proteins for Q3JP68 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JP68 
Go to UniProtKB:  Q3JP68
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JP68
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KD0
Query on KD0

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
Q [auth C],
V [auth D]
3-deoxy-8-O-phosphono-D-manno-oct-2-ulosonic acid
C8 H15 O11 P
RTNBXJBOAIDPME-SHUUEZRQSA-N
A5P
Query on A5P

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
T [auth D]
ARABINOSE-5-PHOSPHATE
C5 H13 O8 P
VJDOAZKNBQCAGE-WDCZJNDASA-N
PEP
Query on PEP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C],
U [auth D]
PHOSPHOENOLPYRUVATE
C3 H5 O6 P
DTBNBXWJWCWCIK-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
M [auth B]
N [auth B]
R [auth C]
H [auth A],
I [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
W [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.84α = 90
b = 146.24β = 90
c = 178.94γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description