3CO8

Crystal structure of alanine racemase from Oenococcus oeni

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

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This is version 1.4 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 Struct Biol Cryst Commun 69: 15-19

  • DOI: 10.1107/S1744309112047276
  • Primary Citation of Related Structures:  
    3CO8

  • 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, with both protomers contributing to the two active sites ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alanine racemaseA, B380Oenococcus oeni PSU-1Mutation(s): 0 
Gene Names: OEOE_0162
EC: 5.1.1.1 (PDB Primary Data), 5.1.1.5 (UniProt)
UniProt
Find proteins for Q04HB7 (Oenococcus oeni (strain ATCC BAA-331 / PSU-1))
Explore Q04HB7 
Go to UniProtKB:  Q04HB7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04HB7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		PYRIDOXAL-5'-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: 1.70 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.397α = 90
b = 99.639β = 103.26
c = 84.67γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2013-01-09
    Changes: Database references
  • Version 1.3: 2013-02-06
    Changes: Database references
  • Version 1.4: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary