The Structural characterization of Burkholderia pseudomallei OppA.

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


A Structure-Based Strategy for Epitope Discovery in Burkholderia Pseudomallei Oppa Antigen.

Lassaux, P.Peri, C.Ferrer-Navarro, M.Gourlay, L.J.Gori, A.Conchillo-Sole, O.Rinchai, D.Lertmemongkolchai, G.Longhi, R.Daura, X.Colombo, G.Bolognesi, M.

(2013) Structure 21: 167

  • DOI: https://doi.org/10.1016/j.str.2012.10.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We present an approach integrating structural and computational biology with immunological tests to identify epitopes in the OppA antigen from the Gram-negative pathogen Burkholderia pseudomallei, the etiological agent of melioidosis. The crystal structure of OppA(Bp), reported here at 2.1 Å resolution, was the basis for a computational analysis that identified three potential epitopes. In parallel, antigen proteolysis and immunocapturing allowed us to identify three additional peptides. All six potential epitopes were synthesized as free peptides and tested for their immunoreactivity against sera from healthy seronegative, healthy seropositive, and recovered melioidosis patients. Three synthetic peptides allowed the different patient groups to be distinguished, underlining the potential of this approach. Extension of the computational analysis, including energy-based decomposition methods, allowed rationalizing results of the predictive analyses and the immunocapture epitope mapping. Our results illustrate a structure-based epitope discovery process, whose application may expand our perspectives in the diagnostic and vaccine design fields.

  • Organizational Affiliation

    Department of Biosciences, University of Milan, Milan 20133, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN506Burkholderia pseudomalleiMutation(s): 0 
Find proteins for Q63ID0 (Burkholderia pseudomallei (strain K96243))
Explore Q63ID0 
Go to UniProtKB:  Q63ID0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63ID0
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OLIGOPEPTIDE DVA3unidentifiedMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.86α = 90
b = 81.93β = 104.34
c = 74.18γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references, Structure summary
  • Version 1.2: 2013-01-23
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description