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Structure of IDP00688

2.37 Angstrom resolution crystal structure of an alanine racemase (alr) from Staphylococcus aureus subsp. aureus COL

Edit deposit information
CSGID target
IDP00688 
PDB Id
3OO2 (NCBI MMDB
Authors
A.S.Halavaty,L.Shuvalova,G.Minasov,J.Winsor,I.Dubrovska,K.Kwon,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Aug 30, 2010 
Release Date
Oct 06, 2010 

Annotation

Description
The structure of alanine racemase from Staphylococcus aureus subsp. aureus COL was determined by X-ray crystallography to a resolution of 2.37 A. The alanine racemase monomer is composed of two domains, an eight-stranded alpha/beta barrel at the N-terminus, which includes residues 1-245, and a C-terminal beta-stranded domain composed of residues 246-382. Protein is dimeric in the crystal with both domains of each chain being involved in dimerization. The N-terminal domain shall bind pyridoxal 5'-phosphate (PLP) cofactor. In the current apo-structure of IDP00688, there is a phosphate ion per each active site that binds at the same place where phosphate group of PLP is positioned in a homologous alanine racemase from Bacillus stearothermophilus (PDB ID 1SFT). Both proteins share about 43 % sequence identity and have 1.5 A rmsd in the position of their C-alpha atoms.  
Functional assignment
Isomerase 

Ligands

Ligand code Name Ligand type
PO4 PHOSPHATE ION crystallization
BME crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=47.73Å, b=118.31Å, c=129.01Å
α=90.00, β=90.00, γ=90.00 
Solvent content
41.73  
Matthews coefficient
2.11  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.59-2.37Å (2.43-2.37Å)  
Rall(%)
20.3 
Rwork(%)
20.0 (25.8) 
Rfree(%)
25.7 (36.5) 
Num. observed reflections
30274 (2145) 
Num. Rfree reflections
1543 (103) 
Completeness(%)
99.5 (99.1) 

Model parameters

Num Atoms
5916  
Num Waters
120  
Num Hetatoms
145  
Model mean isotropic B factor
53.390Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.567°  
Filename uploaded
3OO2.pdb (uploaded on Sep 28, 2011 11:26 AM)  
Inserted
Aug 31, 2010