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Structure of IDP90555

Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni complexed with ADP and Tryptophane

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CSGID target
IDP90555 
PDB Id
3TZL (NCBI MMDB) 
Authors
Y.Kim,M.Zhou,S.Grimshaw,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Sep 27, 2011 
Release Date
Oct 05, 2011 

Annotation

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Description
Tryptophanyl-tRNA Synthetase (TrpS) is involved in protein synthesis and regulation of RNA transcription and translation. It catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA. The structure was produced by co-crystallizing the protein with ADP, however, not only ADP but also Trp were found bound tightly in the active site located in the middle of each subunit of the dimer. 
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
    NA sodium ion crystallization
    PO4 phosphate ion crystallization
    LTR l-tryptophan biological
    ADP adenosine-5'-diphosphate biological
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    P 1 21 1  
    Unit Cell

    a=66.78Å, b=50.63Å, c=105.92Å
    α=90.00, β=107.00, γ=90.00  
    Solvent content
     
    Matthews coefficient
     

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    28.79-2.15Å (2.21-2.15Å)  
    Rall(%)
    18.3  
    Rwork(%)
    18.1 (24.0)  
    Rfree(%)
    21.8 (28.3)  
    Num. observed reflections
    38111 (2299)  
    Num. Rfree reflections
    1901 (113)  
    Completeness(%)
    98.1 (82.0)  

    Model parameters

    Num Atoms
    5135  
    Num Waters
    218  
    Num Hetatoms
    294  
    Model mean isotropic B factor (Å2)
    49.070  
    RMSD bond length (Å)
    0.009  
    RMSD bond angle
    1.189°  
    RMSD dihedral angle
    15.417°
     
    Filename uploaded
    dep.pdb (uploaded on Sep 27, 2011 2:18 PM)  
    Inserted
    Sep 27, 2011