Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 2-phosphoserine

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

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This is version 1.3 of the entry. See complete history


An ensemble of structures of Burkholderia pseudomallei 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase.

Davies, D.R.Staker, B.L.Abendroth, J.A.Edwards, T.E.Hartley, R.Leonard, J.Kim, H.Rychel, A.L.Hewitt, S.N.Myler, P.J.Stewart, L.J.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1044-1050

  • DOI: https://doi.org/10.1107/S1744309111030405
  • Primary Citation of Related Structures:  
    3EZN, 3FDZ, 3GP3, 3GP5, 3GW8, 3LNT

  • PubMed Abstract: 

    Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and Northern Australia. Burkholderia is responsible for melioidosis, a serious infection of the skin. The enzyme 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase (PGAM) catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate, a key step in the glycolytic pathway. As such it is an extensively studied enzyme and X-ray crystal structures of PGAM enzymes from multiple species have been elucidated. Vanadate is a phosphate mimic that is a powerful tool for studying enzymatic mechanisms in phosphoryl-transfer enzymes such as phosphoglycerate mutase. However, to date no X-ray crystal structures of phosphoglycerate mutase have been solved with vanadate acting as a substrate mimic. Here, two vanadate complexes together with an ensemble of substrate and fragment-bound structures that provide a comprehensive picture of the function of the Burkholderia enzyme are reported.

  • Organizational Affiliation

    Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA. ddavies@embios.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
A, B, C, D
257Burkholderia pseudomalleiMutation(s): 0 
Gene Names: gpmABPSL0443
EC: (PDB Primary Data), (UniProt)
Find proteins for Q3JWH7 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JWH7 
Go to UniProtKB:  Q3JWH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JWH7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A]
H [auth B]
K [auth C]
L [auth C]
O [auth D]
E [auth A],
H [auth B],
K [auth C],
L [auth C],
O [auth D],
P [auth D]
C8 H18 O5
Query on SEP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C],
R [auth D]
C3 H8 N O6 P
Query on PO3

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
Q [auth D]
O3 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.263α = 107.96
b = 72.045β = 93
c = 78.036γ = 104.2
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description