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 

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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
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(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
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  • 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

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Entry History 

Deposition Data

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