4B5C

Crystal structure of the peptidoglycan-associated lipoprotein from Burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exploiting the Burkholderia Pseudomallei Acute Phase Antigen Bpsl2765 for Structure-Based Epitope Discovery/Design in Structural Vaccinology.

Gourlay, L.J.Peri, C.Ferrer-Navarro, M.Conchillo-Sole, O.Gori, A.Rinchai, D.Thomas, R.J.Champion, O.L.Michell, S.L.Kewcharoenwong, C.Nithichanon, A.Lassaux, P.Perletti, L.Longhi, R.Lertmemongkolchai, G.Titball, R.W.Daura, X.Colombo, G.Bolognesi, M.

(2013) Chem Biol 20: 1147

  • DOI: 10.1016/j.chembiol.2013.07.010
  • Primary Citation of Related Structures:  
    4B5C

  • PubMed Abstract: 
  • We solved the crystal structure of Burkholderia pseudomallei acute phase antigen BPSL2765 in the context of a structural vaccinology study, in the area of melioidosis vaccine development. Based on the structure, we applied a recently developed method for epitope design that combines computational epitope predictions with in vitro mapping experiments and successfully identified a consensus sequence within the antigen that, when engineered as a synthetic peptide, was selectively immunorecognized to the same extent as the recombinant protein in sera from melioidosis-affected subjects ...

    We solved the crystal structure of Burkholderia pseudomallei acute phase antigen BPSL2765 in the context of a structural vaccinology study, in the area of melioidosis vaccine development. Based on the structure, we applied a recently developed method for epitope design that combines computational epitope predictions with in vitro mapping experiments and successfully identified a consensus sequence within the antigen that, when engineered as a synthetic peptide, was selectively immunorecognized to the same extent as the recombinant protein in sera from melioidosis-affected subjects. Antibodies raised against the consensus peptide were successfully tested in opsonization bacterial killing experiments and antibody-dependent agglutination tests of B. pseudomallei. Our strategy represents a step in the development of immunodiagnostics, in the production of specific antibodies and in the optimization of antigens for vaccine development, starting from structural and physicochemical principles.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE OMPA FAMILY LIPOPROTEINA, B, C138Burkholderia pseudomalleiMutation(s): 0 
UniProt
Find proteins for Q63RA7 (Burkholderia pseudomallei (strain K96243))
Explore Q63RA7 
Go to UniProtKB:  Q63RA7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ63RA7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A],
E [auth B],
F [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.94α = 90
b = 74.95β = 135.28
c = 72.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-14
    Type: Initial release
  • Version 1.1: 2013-11-13
    Changes: Database references
  • Version 1.2: 2017-07-12
    Changes: Refinement description