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Structure of IDP00038

CRYSTAL STRUCTURE OF MICROCIN IMMUNITY PROTEIN MCCF FROM BACILLUS ANTHRACIS STR. AMES

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CSGID target
IDP00038 
PDB Id
3GJZ (NCBI MMDB
Authors
B.Nocek,M.Zhou,K.Kwon,W.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Boguslaw Nocek 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 09, 2009 
Release Date
Apr 14, 2009 

Annotation

Description
The translation inhibitor microcin C7 (MccC7) is a low-molecular-weight, ribosomally encoded peptide antibiotic that is secreted by some strains of Enterobacteriaceae to kill their sensitive bacterial competitors. Microcin gene clusters include six genes, mccABCDEF, which encode proteins involved in maturation, export, and immunity. It was suggested that the sixth gene, MccF, encodes a specific self-immunity protein, making it resistant to the antibiotic microcin. The crystal structure of the MccF protein from Bacillus anthracis str. Ames was determined to 2.1 A. The asymmetric unit contains two molecules, which are associated into a homodimer. Fold analysis reveals close structural similarity to LD-carboxypeptidase, a serine peptidase from Pseudomonas aeruginosa (PDB id 2AUN). Sequence alignment with LD-carboxypeptidase and close homologs of the MccF protein shows conservation of the hydrolytic triad Ser-His-Glu, suggesting that the MccF protein may display the same activity.  
Functional assignment
 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 43  
Unit Cell

a=118.96Å, b=118.96Å, c=55.54Å
α=90.00, β=90.00, γ=90.00 
Solvent content
51.93  
Matthews coefficient
2.56  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
40.00-2.10Å (2.16-2.10Å)  
Rall(%)
18.9 
Rwork(%)
18.7 (26.5) 
Rfree(%)
23.2 (32.2) 
Num. observed reflections
44930 (3272) 
Num. Rfree reflections
2291 (161) 
Completeness(%)
98.9 (97.8) 

Model parameters

Num Atoms
5209  
Num Waters
230  
Num Hetatoms
358  
Model mean isotropic B factor
21.260Å2  
RMSD bond length
0.020Å  
RMSD bond angle
1.689°  
Filename uploaded
rcsb051955.pdb (uploaded on Mar 13, 2009 4:02 PM)  
Inserted
Mar 13, 2009