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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
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS33816,ZP_02067073.1, 327432
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.91 Rfactor 0.2138
    Waters
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    Solvent Content 57.68

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3pay

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    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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