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Structure of IDP00919

The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Edit deposit information
CSGID target
IDP00919 
PDB Id
3I12 (NCBI MMDB
Authors
R.Zhang,N.Maltseva,L.Papazisi,W.Anderson,A.Joachimiak 
Responsible person
Rong-guang Zhang 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jun 25, 2009 
Release Date
Aug 18, 2009 

Annotation

Description
DD-ligases catalyze the synthesis of the D-Ala-D-Ala and D-Ala-D-Ser dipeptides or the D Ala-D-Lac depsipeptide in an early step of peptidoglycan synthesis. Their function is essential for bacterial growth and specific to bacteria, making them attractive targets for the development of novel antibiotics.D-Ala-D-Ala transferase (MurF) are particularly attractive as antibacterial targets, because these enzymes are essential for growth and utilize low-molecular-weight substrates. We have solved the 2.2A structure of this enzyme complexed with the ligands ADP from Enterica serovar typhimurium.Future research should, however, aim at finding more potent inhibitors endowed with the appropriate pharmacokinetic properties that ensure access to their intracellular target. 
Functional assignment
D-Ala-D-Ala transferase  

Ligands

Ligand code Name Ligand type
ADP

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=85.15Å, b=85.81Å, c=230.89Å
α=90.00, β=90.00, γ=90.00 
Solvent content
54.05  
Matthews coefficient
2.68  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
115.47-2.20Å (2.26-2.20Å)  
Rall(%)
20.0 
Rwork(%)
19.7 (22.0) 
Rfree(%)
24.9 (28.9) 
Num. observed reflections
86405 (6232) 
Num. Rfree reflections
4320 (323) 
Completeness(%)
99.9 (98.8) 

Model parameters

Num Atoms
11107  
Num Waters
315  
Num Hetatoms
0  
Model mean isotropic B factor
28.030Å2  
RMSD bond length
0.022Å  
RMSD bond angle
1.976°  
Filename uploaded
IDP919_2pdb.pdb (uploaded on Jun 25, 2009 6:52 PM)  
Inserted
Jun 25, 2009