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The Open Protein Structure Annotation Network
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3hty

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

    Title Crystal structure of hypothetical protein BT_0869 from Bacteroides thetaiotaomicron VPI-5482 (NP_809782.1) at 1.95 A resolution. To be Published
    Site JCSG
    PDB Id 3hty Target Id 392987
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20277,NP_809782.1, 325027 Molecular Weight 10072.02 Da.
    Residues 93 Isoelectric Point 4.82
    Sequence asivgswvepvpglegqvqgikmeeggvassvnmatlvyeswkqegtkliltgksigngqtiefvdtmd ikrltadslvldnqgmeiryakqk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 16
    Resolution (Å) 1.95 Rfree 0.206
    Matthews' coefficent 2.50 Rfactor 0.166
    Waters 1460 Solvent Content 50.74

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam note: The TOPSAN entry for this structure is rather confusing; it suggests that 3hty is essentially a small monomer that has very similar folds to both 1ldq and 1lke. Now SCOP classifies these two into different FOLDs based on the shear of the strands, viz: 1ldq Fold: Streptavidin-like [50875] barrel, closed; n=8, S=10; meander, 1lke Fold: Lipocalins [50813] barrel, closed or opened; n=8, S=12; meander On iterating out a find some overlaps to lipocalins and not to any streptavidins, so I will go with this classification:
    Update: Unfortunately this family on being built found only hypothetical proteins; the info in TOPSAN is not helpful either as nothing seems to be known about the structure. There is a well conserved tryptophan.
    ID DUF3803
    AC PF12702
    Update: Just to let you know that the family is in fact called Lipocalin_3.

     

     

     

    Gene BT_0869 from Bacteriodes thetaiotaomicron VPI-5482 encodes the NP_809782.1 protein with 115 residues. The search results from NCBI sequence alignment cannot provide any further information other than hypothetical protein. A Pfam family, PF12702 - Lipocalin_3, is being constructed for this protein and its homologs.  It has been assigned as a domain of unknown function DUF3803.  The family contains 2 conserved tryptophan residues.

    There are 16 subunits in each asymmetric 3hty unit cell. The crystal interface interaction indicates that the biomolecule of 3hty should be a monomer. The expresssed construct used for structure determination contains residues 23-115 of the full length protein.

     

    3hty-monomer.png

    Figure 1. 3hty structure carries a β-barrel folding core.  The position of the conserved tryptophans (29 and 64) are shown in ball-and-stick with a grey highlight on the strand.  Both tryptophans are located on the inside of the barrel.

     

    FFAS, and SSM searches provide no hits with distant structural homologues for this target. Dali gives very weak hits (Z-scr=7) with the YCEI protein (1Y0G), Diga16 (1LKE) and avidin (1LDQ).  SCOP classifies these hits into different FOLDs based on the shear of the strands, e.g.
    1ldq, Fold: Streptavidin-like [50875], barrel, closed; n=8, S=10; meander
    1lke, Fold: Lipocalins [50813], barrel, closed or opened; n=8, S=12; meander
    There are some sequence overlaps to lipocalins and not to any streptavidins, leading to the designation of the family as Lipocalins_3.
     

     

    392987_2.png

    Figure 2. The 3hty (Green) structure shares some similarity with the folds of 1LDQ (cyan) and 1LKE (magenta).

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

    FileSizeDateAttached by 
     392987_1.png
    No description
    78.29 kB00:17, 28 Feb 2009kevinjinActions
     392987_2.png
    No description
    179.85 kB00:17, 28 Feb 2009kevinjinActions
     3hty-monomer.png
    3hty monomer with tryptophan residues highlighted
    172.99 kB19:36, 19 Mar 2010mmillerActions
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