6WQW | pdb_00006wqw

Thermobacillus composti GH10 xylanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.235 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Transformation of xylan into value-added biocommodities using Thermobacillus composti GH10 xylanase.

Sepulchro, A.G.V.Pellegrini, V.O.A.Briganti, L.de Araujo, E.A.de Araujo, S.S.Polikarpov, I.

(2020) Carbohydr Polym 247: 116714-116714

  • DOI: https://doi.org/10.1016/j.carbpol.2020.116714
  • Primary Citation Related Structures: 
    6WQW

  • PubMed Abstract: 

    Enzymatic transformation of xylans into renewable fuels and value-added products is mediated by xylanases. Here we describe the biochemical and X-ray structural characterization of Thermobacillus composti GH10 xylanase (TcXyn10A) at 2.1 Å resolution aiming to unravel details of its recognition of glucurono- and arabinoxylan at a molecular level. TcXyn10A improves the efficiency of pretreated lignocellulosic biomass hydrolysis by a commercial enzyme cocktail causing a 15.35 % increase in xylose release and 4.38 % glucose release after 24 h of reaction. The enzyme releases predominantly xylobiose and xylotriose, as well as MeGlcA3 × 3 (from beechwood glucuronoxylan) and a range of decorated xylooligosaccharides (XOS) from rye arabinoxylan, with Ara2 × 2 being the major product. The enzyme liberates XOS with the yields of 29.09 % for beechwood glucuronoxylan and 16.98 % for rye arabinoxylan. Finally, TcXyn10A has a high thermal stability, halotolerance, and resistance to ethanol, biochemical properties that can be desirable for a number of industrial applications.


  • Organizational Affiliation
    • Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590, São Carlos, SP, Brazil.

Macromolecule Content 

  • Total Structure Weight: 38.74 kDa 
  • Atom Count: 2,630 
  • Modeled Residue Count: 305 
  • Deposited Residue Count: 334 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-xylanase334Thermobacillus compostiMutation(s): 0 
EC: 3.2.1.8
UniProt
Find proteins for L0EGW1 (Thermobacillus composti (strain DSM 18247 / JCM 13945 / KWC4))
Explore L0EGW1 
Go to UniProtKB:  L0EGW1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0EGW1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XYP
(Subject of Investigation/LOI)

Query on XYP



Download:Ideal Coordinates CCD File
B [auth A]beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.267 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.235 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.264α = 90
b = 81.264β = 90
c = 92.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil423693/2016-6
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil303988/2016-9
Sao Paulo Research Foundation (FAPESP)Brazil2015/13684-0

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-28
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description