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

    Title Crystal structure of SusD homolog (YP_212639.1) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3ejn Target Id 390167
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS7682,YP_212639.1, BIG_773 Molecular Weight 54257.70 Da.
    Residues 473 Isoelectric Point 4.92
    Sequence gnleemnidpdnatqthpkllltqicmnafkrgtdgmyatkkviqadgesadqyykwtrgsfgyydnlr nvqkmgeeaervnapvytaltkffrayyfyeltlrfgdipysqalkgekeeiytpeydaqedvfagilq elreadeilandasvidgdiiyngnstqwrklinsfrlkvlmtlsnhttvgniniasefkniatnsplm nsladngqlvyldqqgnrypqfnaqwsgyymddtfiqrmrerrdprlfifsaqtnkgktegkpiddfss yeggdpaapysdaiikvsegtispindrfrtdpiveptmlmgyaelqqilaeavvrgwisgnaqtyyek girasfsfyethakdyagylnenavaqylkeplvdftqasgteeqieriimqkylvtfyqgnwdsfyeq lrtgypdfrrpagteipkrwmypqgeydnngtnvetaitrqfgagndkinqatwwqkks
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.168
    Matthews' coefficent 2.39 Rfactor 0.154
    Waters 506 Solvent Content 48.55

    Ligand Information


    Google Scholar output for 3ejn
    1. Structure of BT_3984, a member of the SusD/RagB family of nutrient-binding molecules
    C Bakolitsa, Q Xu, CL Rife, P Abdubek - Section F: Structural , 2010 - scripts.iucr.org
    2. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org

    Protein Summary

    YP_212639.1 belongs to the SusD family (PF07980) of extracellular carbohydrate receptors. This very large (>2000) family is present mostly in Bacteroides (only two homologs in proteobacteria), and is strongly overrepresented in human gut microbes (over 100 paralogs in B. thetaionmicron).


    The figure below represents the monomer structure which consists of two subdomains, first containing several TRP-like repeats and second, a helical domain with a novel fold. In vivo, SusD-homologs form complexes with other proteins from their operons, in the Sus operon these are SusC, SusE, SusF and SusG, therefore it is not clear how far the crystallographical or even the in vitro dimer represents a biologically relevant form. A detailed analysis of a SusD structure was recently published (Koropatkin NM, Martens EC, Gordon JI, Smith TJ., Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.Structure. 2008 Jul;16(7):1105-15.)



    YP_212639.1 is a third solved representative of the SusD family, the first (3cgh) solved by JCSG, the second - the actual SusD (3ck7) by Gordon/Smith group at WashU. The figure below shows the superposition of 3cgh (cyan), apo 3ck7 (magenta) and holo 3ckb (yellow) structures of SusD and theYP_212639.1 protein (green).





    The X-ray diffraction data is twinned with the operator  -H-K, K, -L. The final refined twin fraction was determined to be 0.32. Some regions in the structure, especially 303-311, are poorly defined due to the disordered density.


    Ligand Summary




    No references found.

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