2VD8 | pdb_00002vd8

The crystal structure of alanine racemase from Bacillus anthracis (BA0252)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.199 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2VD8

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structures of an Alanine Racemase from Bacillus Anthracis (Ba0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P).

Au, K.Ren, J.Walter, T.S.Harlos, K.Nettleship, J.E.Owens, R.J.Stuart, D.I.Esnouf, R.M.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 327

  • DOI: https://doi.org/10.1107/S1744309108007252
  • Primary Citation Related Structures: 
    2VD8, 2VD9

  • PubMed Abstract: 

    Bacillus anthracis, the causative agent of anthrax, has been targeted by the Oxford Protein Production Facility to validate high-throughput protocols within the Structural Proteomics in Europe project. As part of this work, the structures of an alanine racemase (BA0252) in the presence and absence of the inhibitor (R)-1-aminoethylphosphonic acid (L-Ala-P) have determined by X-ray crystallography to resolutions of 2.1 and 1.47 A, respectively. Difficulties in crystallizing this protein were overcome by the use of reductive methylation. Alanine racemase has attracted much interest as a possible target for anti-anthrax drugs: not only is D-alanine a vital component of the bacterial cell wall, but recent studies also indicate that alanine racemase, which is accessible in the exosporium, plays a key role in inhibition of germination in B. anthracis. These structures confirm the binding mode of L-Ala-P but suggest an unexpected mechanism of inhibition of alanine racemase by this compound and could provide a basis for the design of improved alanine racemase inhibitors with potential as anti-anthrax therapies.


  • Organizational Affiliation
    • Oxford Protein Production Facility, The Henry Wellcome Building for Genomic Medicine, Oxford University, Roosevelt Drive, Oxford OX3 7BN, England.

Macromolecule Content 

  • Total Structure Weight: 89.4 kDa 
  • Atom Count: 7,335 
  • Modeled Residue Count: 773 
  • Deposited Residue Count: 782 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALANINE RACEMASE
A, B
391Bacillus anthracis str. AmesMutation(s): 0 
EC: 5.1.1.1
UniProt
Find proteins for A0A6L7HC45 (Bacillus anthracis)
Explore A0A6L7HC45 
Go to UniProtKB:  A0A6L7HC45
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6L7HC45
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP

Query on PLP



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
D [auth A],
G [auth B],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.199 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.552α = 90
b = 88.365β = 90
c = 138.968γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description