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3iib

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS SB2B at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3iib Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS25917,YP_926796.1, 3.40.630.10, 333145
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.91 Rfactor 0.151
    Waters
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    Solvent Content 57.67

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3iib

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    Protein Summary

    Pfam update: This protein is now in families PF02225.15 PA, PF04389.10 Peptidase_M28 CL0035.

    This protein is present as a monomer in the asymmetric unit of the crystal structure,

    Fig1.png

    but the predicted oligomeric form from crystal packing is a dimer:

    Fig2.png

    Zinc has been modeled at the putative active site (based on other proteins of similar structure and Pfam classification, follow the link in the "Tags" section below for further details on the zinc peptidase crystal structures solved at the JCSG) comprised of residues: His424, His425, His280, Asp292, Asp293, Asp354, Glu326 and Glu327:

    Fig3.png

    There is a cis-peptide bond between Asp292 and Asp293 which suggests that the substrate for this putative zinc-dependent metallopeptidase is a carbohydrate.

    The protein also had an N-terminal signal peptidase which suggests that it is a periplasmic peptidase.

     

     

     

     

     


    Ligand Summary

    Zinc (ZN) ions (possibly co-purified with the protein) have been modeled at the putative active site based on the signal in the fluorescence excitation scan and peaks in the anomalous difference Fourier map at the selenium remote energy. This is expected to the the biochemically relevant ligand since the crystal structure reveals it to be similar in structure to proteins belonging to the PFam clan CL0035 of zinc peptidases.

    Follow the link in the "Tags" section below for further details on the zinc peptidase crystal structures solved at the JCSG.

    Reviews

    References

     

    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
     Fig1.png
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    425.08 kB23:11, 28 May 2009debanuActions
     Fig2.png
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    539.59 kB23:11, 28 May 2009debanuActions
     Fig3.png
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    560.13 kB23:19, 28 May 2009debanuActions
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