3CO8

Crystal structure of alanine racemase from Oenococcus oeni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of alanine racemase from Oenococcus oeni with bound pyridoxal 5'-phosphate.

Palani, K.Burley, S.K.Swaminathan, S.

(2013) Acta Crystallogr.,Sect.F 69: 15-19

  • DOI: 10.1107/S1744309112047276

  • PubMed Abstract: 
  • The crystal structure of alanine racemase from Oenococcus oeni has been determined at 1.7 Å resolution using the single-wavelength anomalous dispersion (SAD) method and selenium-labelled protein. The protein exists as a symmetric dimer in the crystal ...

    The crystal structure of alanine racemase from Oenococcus oeni has been determined at 1.7 Å resolution using the single-wavelength anomalous dispersion (SAD) method and selenium-labelled protein. The protein exists as a symmetric dimer in the crystal, with both protomers contributing to the two active sites. Pyridoxal 5'-phosphate, a cofactor, is bound to each monomer and forms a Schiff base with Lys39. Structural comparison of alanine racemase from O. oeni (Alr) with homologous family members revealed similar domain organization and cofactor binding.


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alanine racemase
A, B
380Oenococcus oeni (strain ATCC BAA-331 / PSU-1)Mutation(s): 0 
EC: 5.1.1.5
Find proteins for Q04HB7 (Oenococcus oeni (strain ATCC BAA-331 / PSU-1))
Go to UniProtKB:  Q04HB7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.397α = 90.00
b = 99.639β = 103.26
c = 84.670γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
ARP/wARPmodel building
SHARPphasing
HKL-2000data scaling
SHELXDphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2013-01-09
    Type: Database references
  • Version 1.3: 2013-02-06
    Type: Database references