3ZS6

The Structural characterization of Burkholderia pseudomallei OppA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.2 of the entry. See complete history


Literature

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: 10.1016/j.str.2012.10.005
  • Primary Citation of Related Structures:  
    3ZS6

  • 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 ...

    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; Consiglio Nazionale delle Ricerche, Institute of Biophysics, University of Milan, Milan 20133, Italy. Electronic address: martino.bolognesi@unimi.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEINA506Burkholderia pseudomalleiMutation(s): 0 
UniProt
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
OLIGOPEPTIDE DVAB3unidentifiedMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

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