3DAH

2.3 A crystal structure of ribose-phosphate pyrophosphokinase from Burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1371/journal.pone.0053851
  • Structures With Same Primary Citation

  • 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 approa ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribose-phosphate pyrophosphokinase
A, B, C
319Burkholderia pseudomallei 1710bMutation(s): 0 
Gene Names: prsABURPS1710b_0753prs
EC: 2.7.6.1
Find proteins for Q3JW86 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JW86
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
A, B
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.966α = 90
b = 123.242β = 90
c = 197.364γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2013-10-30
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description