3CO8 | pdb_00003co8

Crystal structure of alanine racemase from Oenococcus oeni

• PDB DOI: https://doi.org/10.2210/pdb3CO8/pdb

• Classification: ISOMERASE
• Organism(s): Oenococcus oeni PSU-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-03-27 Released: 2008-04-08 
• Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.259 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

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

• PubMed: 23295479 
• DOI: https://doi.org/10.1107/S1744309112047276
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.39 kDa 
• Atom Count: 6,204 
• Modeled Residue Count: 705 
• Deposited Residue Count: 760 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, B	380	Oenococcus oeni PSU-1	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.259 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.397	α = 90
b = 99.639	β = 103.26
c = 84.67	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Palani, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• 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
• Version 1.5: 2025-03-26
  Changes: Data collection, Database references, Structure summary