3GP3

Crystal structure of phosphoglyceromutase from Burkholderia pseudomallei with 2-phosphoserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.268 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

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


Macromolecules
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: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A]
H [auth B]
K [auth C]
L [auth C]
O [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SEP
Query on SEP

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

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
M [auth C],
Q [auth D]
PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
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
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SEPClick on this verticalbar to view details

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
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations