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Structure of IDP01357

The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor str. N16961

Edit deposit information
CSGID target
IDP01357 
PDB Id
3FWX (NCBI MMDB
Authors
R.Zhang,M.Zhou,J.Stam,W.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Rong-guang Zhang 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 19, 2009 
Release Date
Mar 17, 2009 

Annotation

Description
Peptide deformylase is an intracellular target now well-recognized for the design of new antibiotics. The bacterial susceptibility to such a cytoplasmic target primarily depends on the capacity of the compound to reach and accumulate in the cytosol. Human peptide deformylase (hPDF), located in the mitochondria, has recently become a promising target for anti-cancer therapy. Our crystal structures of polypeptide deformylase (PDF) of Vibrio cholerae shows the similarity with that of other bacterials, like E. coli., staphylococcus aureus and thermotoga. 
Functional assignment
polypeptide deformylase 

Ligands

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

Structure information

Unit cell parameters

Space Group
C 2 2 21  
Unit Cell

a=61.30Å, b=61.46Å, c=210.34Å
α=90.00, β=90.00, γ=90.00 
Solvent content
51.92  
Matthews coefficient
2.56  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
105.41-2.00Å (2.05-2.00Å)  
Rall(%)
20.2 
Rwork(%)
20.2 (22.7) 
Rfree(%)
26.2 (28.5) 
Num. observed reflections
27265 (2035) 
Num. Rfree reflections
1363 (106) 
Completeness(%)
99.5 (100.0) 

Model parameters

Num Atoms
2572  
Num Waters
289  
Num Hetatoms
339  
Model mean isotropic B factor
21.810Å2  
RMSD bond length
0.024Å  
RMSD bond angle
1.922°  
Filename uploaded
rcsb051144.pdb (uploaded on Jan 22, 2009 10:35 AM)  
Inserted
Jan 22, 2009