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Structure of IDP90555

Crystal Structure of Tryptophanyl-tRNA Synthetase from Campylobacter jejuni

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CSGID target
IDP90555 
PDB Id
3M5W (NCBI MMDB) 
Authors
Kim, Y., Zhou, M., Hasseman, J., Anderson, W.F., Joachimiak, A., CSGID. 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 14, 2010 
Release Date
Mar 31, 2010 

Annotation

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Description
This enzyme TrpS 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. Among two aminoacyl-tRNA synthetases group, (class I and II), TrpS belongs to class I together with TyrS and forms dimer in the crystal. Each monomer has a N-terminal alpha-beta Rossman fold and a C-terminal alpha-fold. The N-terminal domain interacts with the N-terminal domain of the other chain and the patch formed between the two domains within the chain is for a nucleotide binding. 
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
    SO4 sulfate ion
    GOL glycerol
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    P 1 21 1  
    Unit Cell

    a=66.15Å, b=50.60Å, c=108.64Å
    α=90.00, β=107.61, γ=90.00  
    Solvent content
    47.66  
    Matthews coefficient
    2.35  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    47.81-2.32Å (2.40-2.32Å)  
    Rall(%)
    18.7  
    Rwork(%)
    18.3 (25.0)  
    Rfree(%)
    24.3 (34.0)  
    Num. observed reflections
    31034 (2550)  
    Num. Rfree reflections
    2135 (169)  
    Completeness(%)
    96.7 (86.0)  

    Model parameters

    Num Atoms
    5331  
    Num Waters
    215  
    Num Hetatoms
    0  
    Model mean isotropic B factor (Å2)
    52.790  
    RMSD bond length (Å)
    0.014  
    RMSD bond angle
    1.460°  
    RMSD dihedral angle
    19.57°
     
    Filename uploaded
    dep1w.pdb (uploaded on Mar 15, 2010 7:52 AM)  
    Inserted
    Mar 15, 2010