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Structure of IDP90611

2.25 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine

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CSGID target
IDP90611 
PDB Id
3N2I (NCBI MMDB) 
Authors
Halavaty, A.S., Minasov, G., Shuvalova, L., Winsor, J., Dubrovska, I., Peterson, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
May 18, 2010 
Release Date
Jun 02, 2010 

Annotation

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Description
A thymidylate kinase catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP). This enzyme from Vibrio cholerae O1 biovar eltor str. N16961 was co-crystallized with thymidine. Crystal diffracted to 2.25 Å resolution and a molecular replacement solution was obtained using the structure of the Vibrio cholerae O1 biovar eltor str. N16961 thymidylate kinase (PDB ID 3LV8).  
Functional assignment
Transferase 
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
    THM thymidine biological
    CL chloride ion

    Structure information

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    Unit cell parameters

    Space Group
    I 41 2 2  
    Unit Cell

    a=92.60Å, b=92.60Å, c=231.54Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    47.58  
    Matthews coefficient
    2.35  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    29.64-2.25Å (2.31-2.25Å)  
    Rall(%)
    20.8  
    Rwork(%)
    20.6 (28.9)  
    Rfree(%)
    26.1 (28.6)  
    Num. observed reflections
    24313 (1739)  
    Num. Rfree reflections
    1239 (86)  
    Completeness(%)
    99.9 (99.8)  

    Model parameters

    Num Atoms
    3258  
    Num Waters
    77  
    Num Hetatoms
    113  
    Model mean isotropic B factor (Å2)
    69.840  
    RMSD bond length (Å)
    0.017  
    RMSD bond angle
    1.844°  
    Filename uploaded
    3N2I.pdb (uploaded on Sep 17, 2010 5:56 PM)  
    Inserted
    May 21, 2010