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3snx

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

    Title Crystal structure of a PUTATIVE SUSD-LIKE CARBOHYDRATE BINDING PROTEIN (BT_1439) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.88 A resolution. To be published
    Site JCSG
    PDB Id 3snx Target Id 396204
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS26660,NP_810352.1, BIG_773, 332858 Molecular Weight 51880.55 Da.
    Residues 459 Isoelectric Point 5.29
    Sequence vssdqvavagnaerlfngawynlfeygttyanigyralqcqddmmasdvvsrpkygfnssyqfndvaip sdgrtsfawyliyktidncntaisikgdseelrqaqgqalalrafcylhlvqhyqftylkdkdapcvpi ytepttsgtkpkgkstvaqvyqqifddlnlaqdyltnyvrkgdgqkfkpntdvvnglmaraylltgqwg eaakaaeaarkgyslmtttaeyegfnnisnkewiwgspqtlsqsdasynfyyldatyvgayssfmadph lmdtfvkgdirlplfqwmregylgykkfhmrsddtadlvlmrsaemylieaeakvrdgvaldqavapln tlrtargvgnydvtgktkeqvideilmerrrelwgegfgitdvlrnqkavermalsedmqktevdcwqe ggsfakrnplghwflnfpdgkafsanssyylyaipekeinanpnl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.88 Rfree 0.2073
    Matthews' coefficent 2.36 Rfactor 0.1732
    Waters 385 Solvent Content 47.87

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Target id 396204 belongs to the SusD Pfam family, and this family is represented by 25 structures in the PDB. In symbiotic bacteria, such as Bacteroides thetaiotamicron, there are several paralogs of SusD and this class of protein plays an important role in sugar transport. The polypeptide backone of target id 396204 was traced using Se-MAD. Subsequent analysis of the diffraction data showed that the crystals of this target were pseudo-merohederally twinned in space group P21, and refinement of this target was carried out assuming this pseudo-merohederal twinning with a twin fraction of 0.4.

    Shown below is a ribbons representation of the structure of target id 396204 with the N-terminal end in blue and the C-terminal end in red.

     

    monomer.png

    A DALI structural similarity search shows that target ID 396204 shows similarity to the following:

     

    PDB ID DALI Z-score rmsd (Ang) length of alignment total residues in related structure % sequence identity Description
    3lew 50.5 1.8 440 476 42 Crystal structure of SusD-like carbohydrate binding protein (YP_001298396.1) from Bacteroides vulgatus ATCC 8482 at 1.70 A resolution
    3l22 39,9 2.3 396 396 21 CRYSTAL STRUCTURE OF A SUSD SUPERFAMILY PROTEIN (BF_0597) FROM BACTEROIDES FRAGILIS AT 2.05 A RESOLUTION
    3kez 39.7 2.2 403 447 29 Crystal structure of Putative sugar binding protein (YP_001299726.1) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution
    3mcx 38.9 2.4 407 459 26 Crystal structure of SusD superfamily protein (BT_2365) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.49 A resolution
    3myv 38.9 2.3 403 444 22 Crystal structure of a SusD superfamily protein (BVU_0732) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution
    3jq1 32.8 2.5 387 462 20 Crystal structure of SusD superfamily protein (YP_001297730.1) from Bacteroides vulgatus ATCC 8482 at 1.55 A resolution
    3otn 31.9 2.7 383 471 21 Crystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides distasonis ATCC 8503 at 1.95 A resolution
    3hdx 31.2 2.8 376 456 21 Crystal structure of SusD superfamily protein (NP_809182.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.50 A resolution
    3jys 31.1 2.9 389 479 21 Crystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution
    3ck7 30.5 2.6 380 496 21 B. thetaiotaomicron SusD with alpha-cyclodextrin [Ref]

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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