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Structure of IDP90849

Crystal Structure of Phosphoserine Aminotransferase from Campylobacter jejuni

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CSGID target
IDP90849 
PDB Id
3M5U (NCBI MMDB) 
Authors
Y.Kim,M.Gu,L.Papazisi,W.F.Anderson,A.Joachimiak 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 13, 2010 
Release Date
Apr 07, 2010 

Annotation

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Description
Phosphoserine aminotransferases is a pyridoxal phosphate dependent enzyme converting O-phospho-L-serine and oxoglutarate to 3-phosphonooxypyruvate and L-glutamate in the major phosphorylated serine biosynthesis pathway. The enzyme is part of the aminotransferase class-V family. The protein structure is a dimer with each subunit consisting of a small and a large domains. The large domain spans residues of 64 – 262 with seven-stranded beta-sheets and four alpha-helices all in one side contacting the same region of the other subunit. The rest of the monomer forms the small domain and between the two domains in a relatively wide open surface, a pyridoxal phosphate binds to a largely positively charged shallow patch. 
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
    GOL glycerol
    MES 2-(n-morpholino)-ethanesulfonic acid
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    P 1 21 1  
    Unit Cell

    a=54.74Å, b=105.86Å, c=70.01Å
    α=90.00, β=99.22, γ=90.00  
    Solvent content
    49.17  
    Matthews coefficient
    2.42  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    34.86-2.15Å (2.23-2.15Å)  
    Rall(%)
    17.2  
    Rwork(%)
    16.9 (22.9)  
    Rfree(%)
    22.0 (28.3)  
    Num. observed reflections
    44521 (4092)  
    Num. Rfree reflections
    2248 (223)  
    Completeness(%)
    99.2 (96.0)  

    Model parameters

    Num Atoms
    6191  
    Num Waters
    428  
    Num Hetatoms
    0  
    Model mean isotropic B factor (Å2)
    37.790  
    RMSD bond length (Å)
    0.013  
    RMSD bond angle
    1.355°  
    RMSD dihedral angle
    18.82°
     
    Filename uploaded
    dep1w.pdb (uploaded on Mar 15, 2010 8:07 AM)  
    Inserted
    Mar 15, 2010