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Structure of IDP90771

1.65 Angstrom Resolution Crystal Structure of Type II 3-Dehydroquinate Dehydratase (aroQ) from Yersinia pestis.

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CSGID target
IDP90771 
PDB Id
3LWZ (NCBI MMDB) 
Authors
Minasov, G. Light, S.H. Shuvalova, L. Dubrovska, I. Winsor, J. Papazisi, L. Anderson, W.F. Center for Structural Genomics of Infectious Diseases (CSGID). 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Feb 24, 2010 
Release Date
Mar 09, 2010 

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 catalyzed by two enzyme families which utilize distinct mechanisms. CSGID has solved two structures of the type I enzyme (IDP90163 and IDP90922). Here we present a representative of the dodecameric type II enzyme.  
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
    BME beta-mercaptoethanol crystallization
    GOL glycerol crystallization
    EDO 1,2-ethanediol crystallization

    Structure information

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    Unit cell parameters

    Space Group
    H 3  
    Unit Cell

    a=90.59Å, b=90.59Å, c=216.50Å
    α=90.00, β=90.00, γ=120.00  
    Solvent content
    51.98  
    Matthews coefficient
    2.56  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    29.38-1.65Å (1.69-1.65Å)  
    Rall(%)
    15.1  
    Rwork(%)
    14.9 (22.9)  
    Rfree(%)
    18.2 (26.8)  
    Num. observed reflections
    79598 (5773)  
    Num. Rfree reflections
    3979 (272)  
    Completeness(%)
    99.9 (99.1)  

    Model parameters

    Num Atoms
    4908  
    Num Waters
    682  
    Num Hetatoms
    857  
    Model mean isotropic B factor (Å2)
    20.510  
    RMSD bond length (Å)
    0.012  
    RMSD bond angle
    1.319°  
    Filename uploaded
    rcsb057834.pdb (uploaded on Mar 02, 2010 5:34 PM)  
    Inserted
    Mar 02, 2010