2DY3

Crystal Structure of alanine racemase from Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb2DY3/pdb

• Classification: ISOMERASE
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-09-05 Released: 2007-09-11 
• Deposition Author(s): Miyaguchi, I., Sasaki, C., Kato, R., Oikawa, T., Sugio, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.227 

Starting Model: experimental

Literature

Crystal Structure of Alanine Racemase from Corynebacterium glutamicum at 2.1 A resolution

Miyaguchi, I., Sasaki, C., Kato, R., Oikawa, T., Sugio, S.

To be published.

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,PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 157.87 kDa 
• Atom Count: 11,220 
• Modelled Residue Count: 1,365 
• Deposited Residue Count: 1,444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alanine racemase	A, B, C, D	361	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: alr EC: 5.1.1.1
UniProt
Find proteins for Q8RSU9 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8RSU9  Go to UniProtKB:  Q8RSU9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.384	α = 90
b = 113.612	β = 94.73
c = 88.096	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Miyaguchi, I., Sasaki, C., Kato, R., Oikawa, T., Sugio, S.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description