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The Open Protein Structure Annotation Network
PDB Keyword
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4dsd

    Title Crystal structure of a putative periplasmic protein (BACOVA_05534) from Bacteroides ovatus ATCC 8483 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 4dsd Target Id 416999
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS72258,ZP_02068518.1, 328248 Molecular Weight 14531.88 Da.
    Residues 128 Isoelectric Point 6.95
    Sequence kdvitkdmnqlplparnfinsnftkpqvahikidkdmmestkyevvlmdgteidfdskgnweevsakkg qtvpvsivpgfavnylkahnfvnegvtkverdrkgyeielstglsfkfdkkgkfiktdd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.75 Rfree 0.2145
    Matthews' coefficent 3.07 Rfactor 0.1774
    Waters 247 Solvent Content 59.91

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    This is annotated as a hypothetical protein.

    Note from PFAM:

    This matches our family, DUF2874, PF11396. I built a family then merged the seed with that of the DUF. This is interesting because the DUF is in the PepSY clan, and may be representative of the N-terminal region of YpeB proteins. We look forward to the structure coming through.

     

    A manuscript describing the structure of the homolog with PDB id 3due and structure-based Pfam classification has been published: "The structure of BVU2987 from Bacteroides vulgatus reveals a superfamily of bacterial periplasmic proteins with possible inhibitory function", (2010) Acta Crystallogr.,Sect.F 66: 1265-1273."

     

    The monomer structure in rainbow representation is shown below.

    SP13115C_mon.png

    A preliminary observation of the structure suggests that this protein may be a result of a gene duplication event. The two halves of the protein, indeed allign very well, as shown below.

    SP13115C_NC.png

    This  superposition involves 52 residues with a RMSD of 1.924 A between the N-terminal fragment (residues 21-84 in cyan color) and the C-terminal fragment (residues 85-146 in magenta color).

    Furthermore, the sequence alignment of these fragments shows 25% sequence identity.

    N-term  --KDVITKDMNQLPLPARNFINSN-FTKPQVAHIKIDKDMMESTKYEVVLMDGTEIDFDS
    C-term  SAKKGQTVPVSIVPGFAVNYLKAHNFVNEGVTKVERDR-----KGYEIELSTGLSFKFDK
              *.  *  :. :*  * *::::: *.:  *:::: *:     . **: *  * .:.**.
    
    N-term  KGNWEEV
    C-term  KGKFIKT
            **:: :.
    

     

    The structural homologs of this protein are listed below.

    Top 10 DALI Structural Homologs
     
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 3elg 19.1 1.5 123 126 44 Uncharacterized Periplasmic Protein
    2 3due 18.4 1.5 121 127 36 Putative Periplasmic Protein
    3 3db7 18.1 1.6 121 127 38 Putative Calcium-regulated Periplasmic Protein
    4 3d4e 5.9 2.6 93 162 8 Putative Beta-lactamase Inhibitor Protein
    5 3buu 5.7 3.9 86 220 7 Uncharacterized Lola Superfamily Protein Ne2245
    6 2fkj 5.7 2.9 77 361 13 Outer Surface Protein a
    7 2af5 5.6 4.0 79 292 9 Engineered Outer Surface Protein a (ospa) with Th
    8 3u1w 5.5 5.3 94 248 13 Hypothetical Periplasmic Protein
    9 3bk5 5.3 3.8 87 235 9 Putative Outer Membrane Lipoprotein-sorting Prote

     

    A superposition on 3elg (orange) is shown below.

    SP13115C_3elg.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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