3FDZ

Crystal structure of phosphoglyceromutase from burkholderia pseudomallei 1710b with bound 2,3-diphosphoglyceric acid and 3-phosphoglyceric acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.256 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DG2Click on this verticalbar to view detailsBest fitted 3PGClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


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 mutase257Burkholderia pseudomallei 1710bMutation(s): 0 
Gene Names: BURPS1710b_0662gpmA
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase257Burkholderia pseudomallei 1710bMutation(s): 0 
Gene Names: BURPS1710b_0662gpmA
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.256 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.39α = 106.03
b = 48.48β = 91.54
c = 62.09γ = 107.5
Software Package:
Software NamePurpose
StructureStudiodata collection
MOLREPphasing
REFMACrefinement

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 DG2Click on this verticalbar to view detailsBest fitted 3PGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-13
    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: 2016-07-20
    Changes: Non-polymer description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations