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The Open Protein Structure Annotation Network
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4jrl

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

    Title Crystal structure of a putative glycoside hydrolase (BACOVA_00087) from Bacteroides ovatus ATCC 8483 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 4jrl Target Id 416928
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS76499,ZP_02063147.1, 334659 Molecular Weight 39512.16 Da.
    Residues 355 Isoelectric Point 4.67
    Sequence qdealnseaaidvcsgddvqlanidadskvinvyvnkgadlskqkleftlpqgatikvntpitgdtest ydfseephsrkftvtsedgqwqpvytvnvilaelptlfkfeellttsseydtfyeftpatsqeiskvlq wssgnpgfkltgmansridyptvqvangfkgkavkletrntgdfgamvkmyiaagnlfigtfevenalt nprkatnfgfqfykhpialkgyykfkagevysvegqpqtgkrdkcdiyavmyeaennsimlngdnvfns dklvllariepedivesdewneftihfesvkgreiddtklqngkyklgivlsssvdgayfrgavgstly vdelelicke
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.10 Rfree 0.2202
    Matthews' coefficent 2.76 Rfactor 0.1707
    Waters 166 Solvent Content 55.43

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Annotation It falls immediately into the family Xylanase PF13201. There are several structures for this already, 3hbz, 3s30, 4het, 3hbz a putative glycoside hydrolase, 3s30 a hypothetical glycoside hydrolase (bvu from bacteroides vulgatus) 4het a hypothetical glycoside hydrolase the structure should help elucidate more about the likely function of this particular subgroup of sequences. With the structure we may well be able to pin down which glycoside hydrolase it is likely to be

     

     

    Target id 416928 belongs to the Xylanase Pfam family (PF13201). Shown below is a ribbons representation colored from blue to red in a direction indiciative of the N to C-terminal direction.

    monomer.png

    Acoording to Pfam, This structure represents  a family of putative bacterial xylanases. There is a C-terminal carbohydrate binding domain similar to those of carbohydrate enzymes such as glucanase and xylanase. There is also structural similarity of the N-terminal domain, according  to endo-1,4-beta-xylanase (from Streptomyces sviceus) and beta-xylosidase (from Magnetospirillum magnetotacticum MS-1). The N-terminal domain fold is an immunoglobulin-like beta-sandwich. An NCBI BLAST search of the PDB shows target id 416928 shows 82%, 44%, and 40% sequence id with PDB ID 4HET, 3HBZ [Ref], and 3S30 respectively. These three targets are JCSG structures. A DALI search shows that target id 416928 shows structural similarity with PDB ID 4HET and 3HBZ. These similar structures are two-domain JCSG structures also.

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    A sodium ion and glycerol modeled into the structure

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    References

     

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