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Structure of IDP01482

Peptide deformylase from Vibrio cholerae.

Edit deposit information
CSGID target
IDP01482 
PDB Id
3QU1 (NCBI MMDB
Authors
J.Osipiuk,R.Mulligan,L.Papazisi,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Feb 23, 2011 
Release Date
Mar 09, 2011 

Annotation

Description
In eubacteria as well as in mitochondria and chloroplasts, all nascent polypeptides are synthesized with N-formylmethionine at the N terminus. Peptide deformylase (PDF) is required for the removal of the formyl group at the N terminus in eubacteria. PDF is a metalloenzyme utilizing Fe2+ as catalytic metal whereas the Zn2+ form (presented structure) is nearly inactive. The deletion of the PDF gene was shown to be lethal for Escherichia coli. Formylation/deformylation cycle appears to be a characteristic feature of eubacteria and does not occur in the cytoplasm of eucaryotic cells. Therefore, PDF is an attractive target for the design of new antibiotics. 
Functional assignment
Hydrolase 

Ligands

Ligand code Name Ligand type
CL CHLORIDE ION crystallization
ZN crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 41 21 2  
Unit Cell

a=74.30Å, b=74.30Å, c=127.22Å
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
33.30-1.80Å (1.85-1.80Å)  
Rall(%)
16.9 
Rwork(%)
16.7 (19.1) 
Rfree(%)
20.4 (23.9) 
Num. observed reflections
33662 (2459) 
Num. Rfree reflections
1716 (113) 
Completeness(%)
99.6 (99.8) 

Model parameters

Num Atoms
3103  
Num Waters
306  
Num Hetatoms
0  
Model mean isotropic B factor
22.450Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.625°  
Filename uploaded
idp01482.pdb (uploaded on Feb 23, 2011 1:33 PM)  
Inserted
Feb 23, 2011