4B5C | pdb_00004b5c

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 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1016/j.chembiol.2013.07.010
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 46.16 kDa 
  • Atom Count: 2,930 
  • Modeled Residue Count: 357 
  • Deposited Residue Count: 414 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PUTATIVE OMPA FAMILY LIPOPROTEIN
A, B, C
138Burkholderia 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
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.248 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
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 

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
  • Version 1.3: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description