Structure of IDP91046

Crystal structure of the cytoplasmic domain of vancomycin resistance serine racemase VanTg

Edit deposit information
CSGID target
IDP91046 
PDB Id
4ECL (NCBI MMDB
Authors
P.J.Stogios,Z.Wawrzak,G.Minasov,E.Evdokimova,O.Egorova,J.Cosme,R.Di Leo,M.Krishnamoorthy,D.Meziane-Cherif,P.Courvalin,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Peter Stogios 
Responsible lab
University of Calgary 
Deposition Date
Mar 26, 2012 
Release Date
Apr 18, 2012 

Annotation

Description
Vancomycin antibiotic resistance in Enterococci is mediated by at enzymes of at least six different operons. These enzymes collaborate to alter the normal peptidoglycan layer by converting D-ala-D-ala cross-links into D-ala-D-lac or D-ala-D-ser. These converted peptidoglycan layers are resistant to recognition by vancomycin. In this entry, we present the structure of VanTg, a serine racemase that converts L-serine to D-serine, which is then incorporated into the vancomycin-resistant cell wall. The structure is dimeric, with each chain comprised of a TIM barrel domain and a primarily-beta sheet containing domain. This structure will be studied to understand the mechanism of L-serine recognition. 
Functional assignment
racemase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=78.68Å, b=82.34Å, c=117.47Å
α=90.00, β=90.14, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
19.92-2.02Å (2.04-2.02Å)  
Rall(%)
18.3 
Rwork(%)
18.2 (32.5) 
Rfree(%)
23.3 (36.4) 
Num. observed reflections
194391 (5983) 
Num. Rfree reflections
4004 (130) 
Completeness(%)
98.2 (87.0) 

Model parameters

Num Atoms
11590  
Num Waters
696  
Num Hetatoms
731  
Model mean isotropic B factor
35.540Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.039°  
RMSD dihedral angle
13.287°
 
Filename uploaded
efe0004_refine_154.pdb (uploaded on Mar 26, 2012 3:50 PM)  
Inserted
Mar 26, 2012