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Structure of IDP01207

Crystal Structure of D-alanine--D-Alanine Ligase from Bacillus anthracis complexed with ATP

Edit deposit information
CSGID target
IDP01207 
PDB Id
3R5X (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 20, 2011 
Release Date
Apr 06, 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. An ATP molecule was found in the active site patch formed between the two beta sheets from the middle domain and the the C-terminal domain. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
EDO crystallization
CA crystallization
ATP adenosine-5'-triphosphate biological
MG biological
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=56.34Å, b=68.99Å, c=92.39Å
α=73.36, β=84.96, γ=75.46 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
32.78-2.00Å (2.03-2.00Å)  
Rall(%)
17.9 
Rwork(%)
17.7 (31.8) 
Rfree(%)
22.1 (36.0) 
Num. observed reflections
88326 (2493) 
Num. Rfree reflections
4451 (124) 
Completeness(%)
96.8 (86.0) 

Model parameters

Num Atoms
9489  
Num Waters
750  
Num Hetatoms
890  
Model mean isotropic B factor
59.190Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.284°  
RMSD dihedral angle
16.867°
 
Filename uploaded
dep.pdb (uploaded on Mar 20, 2011 3:41 PM)  
Inserted
Mar 20, 2011