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Structure of IDP90711

Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni subsp. jejuni NCTC 11168

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CSGID target
IDP90711 
PDB Id
3LER (NCBI MMDB) 
Authors
Kim, Y., Zhou, M., Hasseman, J., Anderson, W.F., Joachimiak, A. CSGID 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 15, 2010 
Release Date
Jan 26, 2010 

Annotation

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Description
Dihydrodipicolinate synthase (DHDPS), a member of lyase, catalyses the reaction converting L-aspartate 4-semialdehyde and pyruvate to (S)-2,3-dihydropyridine-2,6-dicarboxylate and water. DHDPS from C. jejuni has a TIM barrel structure like all other family proteins which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue (Lys-166) in the barrel. DHDPS is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants.  
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
    MCL nz-(1-carboxyethyl)-lysine biological
    EDO 1,2-ethanediol
    MG unknown
    FMT formic acid
    PEG di(hydroxyethyl)ether
    ACY acetic acid
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    P 21 21 21  
    Unit Cell

    a=72.19Å, b=85.30Å, c=199.16Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    46.43  
    Matthews coefficient
    2.3  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    39.21-1.84Å (1.91-1.84Å)  
    Rall(%)
    15.4  
    Rwork(%)
    15.2 (18.8)  
    Rfree(%)
    19.0 (24.0)  
    Num. observed reflections
    112459 (10600)  
    Num. Rfree reflections
    5611 (519)  
    Completeness(%)
    99.8 (100.0)  

    Model parameters

    Num Atoms
    10463  
    Num Waters
    1100  
    Num Hetatoms
    0  
    Model mean isotropic B factor (Å2)
    31.870  
    RMSD bond length (Å)
    0.013  
    RMSD bond angle
    1.369°  
    RMSD dihedral angle
    19.17°
     
    Filename uploaded
    dep1w.pdb (uploaded on Jan 16, 2010 6:39 PM)  
    Inserted
    Jan 16, 2010