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Structure of IDP90564

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium ion

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CSGID target
IDP90564 
PDB Id
3M6L (NCBI MMDB) 
Authors
Nocek, B., Makowska-Grzyska, M., Maltseva, N., Grimshaw, S., Anderson, W., Joachimiak, A., CSGID 
Responsible person
Boguslaw Nocek 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 15, 2010 
Release Date
Apr 28, 2010 

Annotation

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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
    R5P ribose-5-phosphate biological
    GOL glycerol
    TPP thiamine diphosphate
    CA calcium ion
    EDO 1,2-ethanediol
    PO4 phosphate ion
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    C 1 2 1  
    Unit Cell

    a=130.92Å, b=71.46Å, c=69.62Å
    α=90.00, β=109.48, γ=90.00  
    Solvent content
    43.58  
    Matthews coefficient
    2.18  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    40.00-1.59Å (1.63-1.59Å)  
    Rall(%)
    16.2  
    Rwork(%)
    16.0 (30.5)  
    Rfree(%)
    20.1 (31.6)  
    Num. observed reflections
    76498 (4137)  
    Num. Rfree reflections
    3824 (221)  
    Completeness(%)
    94.3 (69.7)  

    Model parameters

    Num Atoms
    5535  
    Num Waters
    565  
    Num Hetatoms
    0  
    Model mean isotropic B factor (Å2)
    15.950  
    RMSD bond length (Å)
    0.022  
    RMSD bond angle
    2.170°  
    Filename uploaded
    TK-4_refmac1_FINAL-0315.pdb (uploaded on Mar 16, 2010 7:25 PM)  
    Inserted
    Mar 16, 2010