Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 86387.38 
• Atom Count: 5578 
• Residue Count: 760 
• Unique protein chains: 1

3CO8

Crystal structure of alanine racemase from Oenococcus oeni

• DOI: 10.2210/pdb3CO8/pdb

• Classification: ISOMERASE
• Organism(s): Oenococcus oeni (strain ATCC BAA-331 / PSU-1)
• Expression System: Escherichia coli BL21(DE3)


• 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: 1.7 Å
• R-Value Free: 0.259 
• R-Value Work: 0.247 

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

• PubMed: 23295479 
• 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, 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Alanine racemase	A, B	380	Oenococcus 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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 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: 1.7 Å
• R-Value Free: 0.259 
• R-Value Work: 0.247 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 47.397	α = 90.00
b = 99.639	β = 103.26
c = 84.670	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-27 
• 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
  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