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Structure of IDP02135

Crystal Structure of Putative Aspartate Racemase from Salmonella Typhimurium

Edit deposit information
CSGID target
IDP02135 
PDB Id
3S81 (NCBI MMDB
Authors
N.Maltseva,Y.Kim,K.Kwon,R.Zhang,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
May 27, 2011 
Release Date
Jun 15, 2011 

Annotation

Description
D-stereoisomers of amino acids are synthesized from L-stereoisomers by amino acid racemases which catalyze a proton-transfer reaction to invert a chiral center C(alpha) of an amino acid. Crystal Structure of PLP-independent Putative Aspartate Racemase from Salmonella Typhimurium was solved at 1.8A resolution. Its function is independent of metals or cofactors and two cysteins in the active site work as acid and base for racemization assisted by several other residues from the active site. Protein has two structurally very similar domains in a pseudo symmetrical arrangement (residues 1-110, 215-244 form N-terminal and 111-214 - C-terminal domains) situated at approximately 90o to each other. The active site of the protein is situated between domains, where ligand is positioned in the center of the pseudo-symmetry. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
CL crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 32  
Unit Cell

a=84.15Å, b=84.15Å, c=114.57Å
α=90.00, β=90.00, γ=120.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
45.04-1.80Å (1.83-1.80Å)  
Rall(%)
14.3 
Rwork(%)
14.0 (24.1) 
Rfree(%)
16.9 (25.0) 
Num. observed reflections
88730 (4127) 
Num. Rfree reflections
4427 (227) 
Completeness(%)
99.8 (93.0) 

Model parameters

Num Atoms
7222  
Num Waters
661  
Num Hetatoms
716  
Model mean isotropic B factor
29.450Å2  
RMSD bond length
0.006Å  
RMSD bond angle
1.176°  
RMSD dihedral angle
12.391°
 
Filename uploaded
dep0.pdb (uploaded on Jun 01, 2011 2:28 PM)  
Inserted
Jun 01, 2011