Home    Target List    Selection    Community Requests    Clones    XML files    Diffraction Images    Progress    Homolog Search    Clustering    Statistics    News    Help    Log In
To see full content of that page you need the activeISee plugin.
Get the latest version from here.

Structure of IDP90671

Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni in complex with pyridoxine-5'-phosphate.

(tree view)
Edit deposit information
CSGID target
IDP90671 
PDB Id
3O6D (NCBI MMDB) 
Authors
Osipiuk, J., Zhou, M., Kwon, K., Anderson, W., Joachimiak, A. 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jul 28, 2010 
Release Date
Aug 11, 2010 

Annotation

Edit this annotation | Download molsoft presentation
Description
Pyridoxal phosphate biosynthetic protein PdxJ is involved in the de novo synthesis of pyridoxal 5'-phosphate (Vitamin B6). Vitamin B6 is necessary for over 100 enzymatic reactions. It is also implicated in numerous human body functions ranging from modulation of hormone function to its recent discovery as a potent antioxidant. Its de novo biosynthesis occurs only in bacteria, fungi and plants. PdxJ protein catalyzes the condensation of 1-deoxy-D-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxal 5'-phosphate. PdxJ is a potential target for the development of new antibiotics due to its absence in mammals. 
Functional assignment
Transferase 
Slides:
  • Asymmetric unit
  • Biological unit
  • B-factors distribution
  • B-factors distribution on the surface
  • Homolog superposition
    • Presentation Controlls:
    rotate
    with the [Left]-mouse
    drag
    with the [Middle]-mouse (or with [Ctrl]-key pressed)
    zoom
    with the [Left]-mouse in the left zone of the window: zoom-up, unzoom-down
    clipping
    with the [Left]-mouse in the right zone of the window

    Presentation Options:
    background color:
    black, white
    ribbon style:
    normal, smooth
    ribbon color:
    secondary structure, N to C, molecule

    Ligands

    Ligand code Name Ligand type
    PXP pyroxidine-5'-phosphate biological
    PO4 phosphate ion
    MSE selenomethionine modified residue

    Structure information

    View structure information | Edit structure information (upload a PDB file)

    Unit cell parameters

    Space Group
    I 4 2 2  
    Unit Cell

    a=90.24Å, b=90.24Å, c=156.08Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    54.37  
    Matthews coefficient
    2.7  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    32.00-1.95Å (2.00-1.95Å)  
    Rall(%)
    17.1  
    Rwork(%)
    17.0 (23.8)  
    Rfree(%)
    19.7 (30.4)  
    Num. observed reflections
    23841 (1720)  
    Num. Rfree reflections
    1215 (92)  
    Completeness(%)
    99.5 (99.7)  

    Model parameters

    Num Atoms
    2285  
    Num Waters
    113  
    Num Hetatoms
    0  
    Model mean isotropic B factor (Å2)
    23.930  
    RMSD bond length (Å)
    0.019  
    RMSD bond angle
    1.594°  
    Filename uploaded
    idp90671_pxp.pdb (uploaded on Jul 28, 2010 8:27 PM)  
    Inserted
    Jul 28, 2010