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Structure of IDP01207

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis

Edit deposit information
CSGID target
IDP01207 
PDB Id
3R23 (NCBI MMDB
Authors
Y.Kim,R.Mulligan,J.Hasseman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 12, 2011 
Release Date
Mar 30, 2011 

Annotation

Description
This enzyme belongs to the family of ligases, specifically those forming carbon-nitrogen bonds as acid-D-amino-acid ligases and participates in d-alanine metabolism and peptidoglycan biosynthesis. The 2.0 A crystal structure of D-alanine--D-alanine ligase from Bacillus anthracis complexed with ATP revealed a dimer with each monomer consisting of three alpha-beta domains. The active site patch is formed between the two beta sheets, one each from the middle domain and the the C-terminal domain.  
Functional assignment
 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=65.88Å, b=83.19Å, c=128.38Å
α=90.00, β=90.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
40.24-2.49Å (2.58-2.49Å)  
Rall(%)
19.7 
Rwork(%)
19.1 (22.3) 
Rfree(%)
25.6 (33.8) 
Num. observed reflections
26525 (2252) 
Num. Rfree reflections
2161 (184) 
Completeness(%)
96.8 (90.0) 

Model parameters

Num Atoms
4755  
Num Waters
234  
Num Hetatoms
234  
Model mean isotropic B factor
44.890Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.518°  
RMSD dihedral angle
16.891°
 
Filename uploaded
dep.pdb (uploaded on Mar 20, 2011 12:06 AM)  
Inserted
Mar 20, 2011