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Structure of IDP90646

Crystal Structure of Probable Cytoplasmic L-asparaginase fromCampylobacter jejuni

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CSGID target
IDP90646 
PDB Id
3NXK (NCBI MMDB) 
Authors
Kim, Y., Makowska-Grzyska, M., Maltseva, N., Papazisi, L., Anderson, W.F., Joachimiak, A., CSGID 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jul 14, 2010 
Release Date
Aug 04, 2010 

Annotation

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Description
L-Asparaginase, which is found in various plant, animal and bacterial cells, catalyses the deamination of asparagine to yield aspartic acid and an ammonium ion, resulting in a depletion of free circulatory asparagine in plasma. The structure of the asparaginase from Campylobacter jejuni forms a tight homotetramer, dimer of intimate dimers with 222 symmetry similar to that of L-asparaginase from Erwinia chrysanthemi. Each of the four active sites of l-asparaginase is located between the N- and C-terminal domains of two adjacent monomers. The flexible part of the active site consists of several residues (positions 16−34), referred to as the active site flexible loop, and covers the binding pocket upon substrate binding to the enzyme. The nucleophile, Thr16, is also located in the flexible loop region. 
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
    ACY acetic acid
    GOL glycerol
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    P 1 21 1  
    Unit Cell

    a=73.32Å, b=127.65Å, c=149.83Å
    α=90.00, β=103.05, γ=90.00  
    Solvent content
    48.15  
    Matthews coefficient
    2.37  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    36.91-2.40Å (2.48-2.40Å)  
    Rall(%)
    16.9  
    Rwork(%)
    16.6 (23.3)  
    Rfree(%)
    22.8 (30.4)  
    Num. observed reflections
    109638 (10070)  
    Num. Rfree reflections
    5470 (457)  
    Completeness(%)
    99.5 (96.0)  

    Model parameters

    Num Atoms
    20585  
    Num Waters
    1060  
    Num Hetatoms
    72  
    Model mean isotropic B factor (Å2)
    35.530  
    RMSD bond length (Å)
    0.008  
    RMSD bond angle
    1.117°  
    RMSD dihedral angle
    14.462°
     
    Filename uploaded
    dep1w.pdb (uploaded on Jul 14, 2010 6:27 AM)  
    Inserted
    Jul 14, 2010