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The Open Protein Structure Annotation Network
PDB Keyword
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3kst

    Title Crystal structure of Endo-1,4-beta-xylanase (NP_811807.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3kst Target Id 396207
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS25883,NP_811807.1, _0029.002555_, 332845 Molecular Weight 34090.33 Da.
    Residues 305 Isoelectric Point 5.04
    Sequence tddeekdnngqgsvsvetnylpiadpyvmfynnkyyaygtggttagegfacfssddlknwkregqalsa tdsygtwgfwapevyyveskkkfylfysaeehicvatsttpegpfrqevkqpiwseksidtslfidddg tpylyfvrftdgnviwvaqmtddlmsiktetlnqcikaevswellqgkvaegpsllkkngvyyliysan hyenkgygvgyatsdtpmgpwvkysknpllqgdaatglvgtghgapfqckdgswkyifhahwsaaeiqp rtsyikdfaisdqgvvtisgtvikprvlk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.179
    Matthews' coefficent 2.36 Rfactor 0.145
    Waters 514 Solvent Content 47.94

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3kst
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     

    Protein Summary

    The protein NP_811807.1 is annotated as Endo-1,4-beta-xylanase. NP_811807.1 belongs to PFAM PF04616 Glyco_hydro_43 which contains members that are arabinanase. Rabinanases hydrolyses the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The structure of arabinanase Arb43A from Cellvibrio japonicus reveals a five-bladed beta-propeller fold. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller.

    The monomer structure, similar to structures in this PFAM,  is shown below with a Calcium ion bound in the center of the protein.

    PX15502A.png

    The Calcium ion is engaged in several interactions with the protein, shown below.

    PX15502A_CA.png

     

    There are several structural homologs:

    DALI Structural Homologs

    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 3cpn 31.6 2.2 264 319 20 BETA-XYLOSIDASE, FAMILY 43 GLYCOSYL HYDROLASE
    2 1gyh 30.2 2.2 263 317 24 ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
    3 1gye 30.2 2.2 262 315 24 ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
    4 1gyd 30.0 2.2 262 315 24 ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE A
    5 2exk 29.3 2.4 265 533 23 BETA-D-XYLOSIDASE
    6 2exi 29.2 2.4 265 533 24 BETA-D-XYLOSIDASE
    7 2exh 29.2 2.4 265 533 24 BETA-D-XYLOSIDASE
    8 1yi7 29.2 2.5 268 534 22 BETA-XYLOSIDASE, FAMILY 43 GLYCOSYL HYDROLASE
    9 1y7b 29.2 2.5 268 534 22 BETA-XYLOSIDASE, FAMILY 43 GLYCOSYL HYDROLASE
    10 2exj 29.1 2.4 265 533 23 BETA-D-XYLOSIDASE

     

     A superposition of the structures are shown below.

    PX15502A_1gyh_3cpn.png NP_811807.1 (green), 1gyh (cyan), 3cpn (lime)
     

    PX15502A_others.pngNP_811807.1 (green), 1y7b (lightmagenta), 1yi7 (yellow), 2exh (salmon), 2exi (lightgrey), 2exj (slate), 2exk (orange)

     

     

     

    Refinement Notes:

    The diffraction data for this crystal is twinned. The data were initially processed, solved and traced in space group C2. Later, the true space group P21 was recognized during refinement and subsequently the data were re-integrated and refined in P21. The refined twin fraction is 0.4806 with the twin law "-L, -K, -H".

     

    Literature references

    1. Nurizzo D, Turkenburg JP, Charnock SJ, Roberts SM, Dodson EJ, McKie VA, Taylor EJ, Gilbert HJ, Davies GJ; , Nat Struct Biol 2002;9:665-668.: Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold. PUBMED:12198486

    Ligand Summary

    Reviews

    References

     

    No references found.

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