3ZS6

The Structural characterization of Burkholderia pseudomallei OppA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 

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

  • 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 str ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN
A
506Burkholderia pseudomallei (strain K96243)Mutation(s): 0 
Gene Names: oppA
Find proteins for Q63ID0 (Burkholderia pseudomallei (strain K96243))
Go to UniProtKB:  Q63ID0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
OLIGOPEPTIDE DVA
B
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.860α = 90.00
b = 81.930β = 104.34
c = 74.180γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-04
    Type: Initial release
  • Version 1.1: 2013-01-09
    Type: Database references, Structure summary
  • Version 1.2: 2013-01-23
    Type: Database references