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Structure of IDP00523

Crystal Structure of Beta-lactamase/D-alanine Carboxypeptidase from Yersinia pestis complexed with citrate

Edit deposit information
CSGID target
IDP00523 
PDB Id
3RJU (NCBI MMDB
Authors
Y.Kim,M.Zhou,M.Gu,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Apr 15, 2011 
Release Date
Apr 27, 2011 

Annotation

Description
Beta-lactam is a common element of a group of antibiotics so-called beta-lactam antibiotics such as penicillins, cephamycins, and carbapennems. Beta-lactamses, produced by some bacteria, are responsible for the resistance to these antibiotics. The beta-lactamase from Y. pestis is a monomer, the overall structure is similar to those of other class C beta-lactamse and all catalytic residues are also in the similar locations in the conserved active site. Lactamase breaks down a beta-lactam by opening the four-atom ring. The protein was co-crystallized in the presence of Ala-Ala, however, citrate molecule which was not included in the crystallization, was found in the active site. 
Functional assignment
hydrolase 

Ligands

Ligand code Name Ligand type
CIT citrate biological
MSE selenomethionine 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=43.16Å, b=75.48Å, c=59.07Å
α=90.00, β=103.93, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.51-1.50Å (1.53-1.50Å)  
Rall(%)
15.7 
Rwork(%)
15.6 (26.8) 
Rfree(%)
17.7 (29.7) 
Num. observed reflections
59809 (2156) 
Num. Rfree reflections
3014 (119) 
Completeness(%)
96.8 (74.0) 

Model parameters

Num Atoms
2794  
Num Waters
537  
Num Hetatoms
568  
Model mean isotropic B factor
17.630Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.330°  
RMSD dihedral angle
14.043°
 
Filename uploaded
dep.pdb (uploaded on May 10, 2011 5:50 PM)  
Inserted
May 10, 2011