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Structure of IDP90572

Crystal Structure of Methionyl-tRNA Formyltransferase fromYersinia pestis complexed with L-methionine

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CSGID target
IDP90572 
PDB Id
3R8X (NCBI MMDB) 
Authors
N.Maltseva,Y.Kim,J.Hasseman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 24, 2011 
Release Date
Apr 13, 2011 

Annotation

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Description
Methionyl-tRNA(fMet) formyltransferase is important in translation initiation in prokariotes since it is responsible for the formylation of the methionyl moiety esterified to the 3' end of tRNA. It transfers 10-formyltetrahydrofolate to the L-methionyl-tRNA(fMet) which results in production of tetrahydrofolate and N-formylmethionyl-tRNA(fMet). Inactivation of this gene in Escherichia coli severely impairs growth of bacteria. Crystal Structure of Methionyl-tRNA Formyltransferase from Yersinia pestis complexed with L-methionine was solved at 2.26A resolution. The enzyme is composed of two domains (N-terminal 1-204 and C-terminal 213-314 ) with a short linker 205- 212 between them. Residues from 41 to 46 are disordered in the structure. L –methionine is situated in the N-terminal part of the protein in a cavity and coordinated by Asn109, His111, Gly120 and Asp147. 
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
    GOL glycerol crystallization
    EMM [methyl(vinyl)amino]methanol crystallization
    TRS 2-amino-2-hydroxymethyl-propane-1,3-diol crystallization

    Structure information

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    Unit cell parameters

    Space Group
    P 43 2 2  
    Unit Cell

    a=62.75Å, b=62.75Å, c=172.64Å
    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
    42.97-2.26Å (2.29-2.25Å)  
    Rall(%)
    18.0  
    Rwork(%)
    17.7 (21.8)  
    Rfree(%)
    23.1 (29.1)  
    Num. observed reflections
    17851 (2737)  
    Num. Rfree reflections
    901 (141)  
    Completeness(%)
    99.6 (99.0)  

    Model parameters

    Num Atoms
    2474  
    Num Waters
    142  
    Num Hetatoms
    165  
    Model mean isotropic B factor (Å2)
    35.870  
    RMSD bond length (Å)
    0.010  
    RMSD bond angle
    1.395°  
    RMSD dihedral angle
    15.44°
     
    Filename uploaded
    dep2.pdb (uploaded on Mar 24, 2011 3:35 PM)  
    Inserted
    Mar 24, 2011