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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

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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
 
Slides:
  • Asymmetric unit
  • Biological unit
  • B-factors distribution
  • B-factors distribution on the surface
  • Homolog superposition
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    secondary structure, N to C, molecule

    Ligands

    Ligand code Name Ligand type
    MSE selenomethionine modified residue

    Structure information

    View structure information | Edit structure information (upload a PDB file)

    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 (Å2)
    21.260  
    RMSD bond length (Å)
    0.020  
    RMSD bond angle
    1.689°  
    Filename uploaded
    rcsb051955.pdb (uploaded on Mar 13, 2009 4:02 PM)  
    Inserted
    Mar 13, 2009