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Structure of IDP90922

1.85 Angstrom Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella typhimurium LT2.

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CSGID target
IDP90922 
PDB Id
3L2I (NCBI MMDB) 
Authors
G.Minasov,S.H.Light,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Dec 15, 2009 
Release Date
Dec 29, 2009 

Annotation

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Description
The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, a precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in humans, making it an attractive target for the development of novel antibiotics. The third step in the pathway consists of the dehydration of dehydroquinate to dehydroshikimate. This reaction can be achieved independently by two distinct enzyme families. The protein structure presented here is representative of the type I enzyme. The structure displays a typical TIM barrel fold with eight parallel beta strands and a C-terminal active site. In its unliganded form a three residues near the active site are disordered and have not been modeled. 
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
    MG magnesium ion crystallization

    Structure information

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    Unit cell parameters

    Space Group
    P 21 21 21  
    Unit Cell

    a=36.92Å, b=76.91Å, c=171.85Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    39.3  
    Matthews coefficient
    2.03  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    28.64-1.85Å (1.90-1.85Å)  
    Rall(%)
    17.0  
    Rwork(%)
    16.8 (21.0)  
    Rfree(%)
    21.4 (29.1)  
    Num. observed reflections
    42787 (3010)  
    Num. Rfree reflections
    2139 (162)  
    Completeness(%)
    99.9 (98.6)  

    Model parameters

    Num Atoms
    4119  
    Num Waters
    443  
    Num Hetatoms
    453  
    Model mean isotropic B factor (Å2)
    17.920  
    RMSD bond length (Å)
    0.016  
    RMSD bond angle
    1.526°  
    Filename uploaded
    rcsb056750.pdb (uploaded on Jan 06, 2010 12:53 PM)  
    Inserted
    Jan 06, 2010