4CV7

Crystal structure of Rhodococcus equi VapB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of Rhodococcus Equi Virulence-Associated Protein B (Vapb) Reveals an Eight-Stranded Antiparallel [Beta]-Barrel Consisting of Two Greek-Key Motifs

Geerds, C.Wohlmann, J.Haas, A.Niemann, H.H.

(2014) Acta Crystallogr.,Sect.F 70: 866

  • DOI: 10.1107/S2053230X14009911

  • PubMed Abstract: 
  • Members of the virulence-associated protein (Vap) family from the pathogen Rhodococcus equi regulate virulence in an unknown manner. They do not share recognizable sequence homology with any protein of known structure. VapB and VapA are normally asso ...

    Members of the virulence-associated protein (Vap) family from the pathogen Rhodococcus equi regulate virulence in an unknown manner. They do not share recognizable sequence homology with any protein of known structure. VapB and VapA are normally associated with isolates from pigs and horses, respectively. To contribute to a molecular understanding of Vap function, the crystal structure of a protease-resistant VapB fragment was determined at 1.4 Å resolution. The structure was solved by SAD phasing employing the anomalous signal of one endogenous S atom and two bound Co ions with low occupancy. VapB is an eight-stranded antiparallel β-barrel with a single helix. Structural similarity to avidins suggests a potential binding function. Unlike other eight- or ten-stranded β-barrels found in avidins, bacterial outer membrane proteins, fatty-acid-binding proteins and lysozyme inhibitors, Vaps do not have a next-neighbour arrangement but consist of two Greek-key motifs with strand order 41238567, suggesting an unusual or even unique topology.


    Organizational Affiliation

    Department of Chemistry, Bielefeld University, Universitaetsstrasse 25, 33615 Bielefeld, Germany.,Institute for Cell Biology, University of Bonn, Ulrich-Haberland Strasse 61a, 53121 Bonn, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VIRULENCE ASSOCIATED PROTEIN VAPB
A
113Rhodococcus hoagiiMutation(s): 0 
Find proteins for B4F366 (Rhodococcus hoagii)
Go to UniProtKB:  B4F366
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.170 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 83.820α = 90.00
b = 83.820β = 90.00
c = 49.130γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-07-09
    Type: Database references
  • Version 1.2: 2014-07-23
    Type: Database references
  • Version 1.3: 2019-03-06
    Type: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-08
    Type: Data collection, Experimental preparation