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3pay

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

    Title Crystal structure of a putative adhesin (BACOVA_04077) from Bacteroides ovatus at 2.50 A resolution. To be published
    Site JCSG
    PDB Id 3pay Target Id 416713
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS33816,ZP_02067073.1, 327432 Molecular Weight 35666.39 Da.
    Residues 313 Isoelectric Point 4.69
    Sequence scdsiredlprcelwlefvfdynmeyadafnpqvksvdvlvfdsddkllftksvkvaalvggnrmsltd eldfgsykvltvgslsdrfrlsdnagnklvpgtttlqqvivslkretggvnfefqhlyfgevvevdhlp sntnhkiypvnlirdtnrfnlalmgyeenkvdgtqytfeiqapenavysweneptgqgpityvpyytgp geisdvvmsarlntmrllnrsgwdykfiirdanteaevwsynlmtllsiarpvsrydgtelpfqeyldr qsewnlvftvvekngggflqigivvgtwihwlhgmev
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.50 Rfree 0.2394
    Matthews' coefficent 2.91 Rfactor 0.2138
    Waters 239 Solvent Content 57.68

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3pay

    Protein Summary

    The structure of target ID 416713 was determined from a triclinic (P1) crystal form at a resolution of 2.5 Angstroms using three wavelength Se-MAD methods. The target is a member of  the DUF1812 (Pfam 08842) Pfam family. Shown below is a ribbons representation of the monomer with the N-terminal end in blue and the C-terminal end in red.

     

    monomer.png

     

    The overall structure can be described as two tandemly repeating beta-sandwich domains, and is similar to another JCSG structure,  PDB ID 3gf8. Howeber, a significant structural difference between target ID 416713 and PDB ID 3gf8 is that the former shows a disulfide bond covalently linking the sidechains of Cys 21 and Cys 31 at the N-terminal end. A similar disulfide bond is absent in PDB ID 3gf8. Calcium acetate was included in the crystallization of target ID 416713, and the crystals structure indicates that Ca2+ is bound on the C-terminal domains to two of the subunits in the asymmetric unit.

    Crystal packing suggests that a tetramer is a oligomeric state for this target id 416713. Shown below is a ribbons representation of the tetramer discerned from the crystal structure.

     

    tetramer.png

     A DALI structural similarity search shows that target ID 416173 has structural similarity to the following:

     

    PDB ID
    DALI Z-Score
    rmsd (Ang)
    residue length of alignment
    total number of residues in related target
    sequence id (%)
    Description
    3gf8 28.1 2.2 265 284 32 Putative Polysaccharide Binding Protein (DUF1812)(NP_809975.1)  from Bacteroides thetaiotaomicron at 2.20 Ang.
    3liu 10.1 4.3 215 373 10 Putative Cell Adhesion Protein (YP_00130480.1) from Parabacteroides distasonis at 2.05 Ang.

     

     

     

    Shown below is a comparison of the crytsral structures of target id 416713 (green) with that of PDB ID 3gf8 (yellow)

    3gf8_comparison.png

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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