1F5J

CRYSTAL STRUCTURE OF XYNB, A HIGHLY THERMOSTABLE BETA-1,4-XYLANASE FROM DICTYOGLOMUS THERMOPHILUM RT46B.1, AT 1.8 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of XynB, a highly thermostable beta-1,4-xylanase from Dictyoglomus thermophilum Rt46B.1, at 1.8 A resolution.

McCarthy, A.A.Morris, D.D.Bergquist, P.L.Baker, E.N.

(2000) Acta Crystallogr.,Sect.D 56: 1367-1375


  • PubMed Abstract: 
  • Microorganisms employ a large array of enzymes to break down the cellulose and hemicelluloses of plant biomass. These enzymes, especially those with high thermal stability, have many uses in biotechnology. We have solved the crystal structure of a be ...

    Microorganisms employ a large array of enzymes to break down the cellulose and hemicelluloses of plant biomass. These enzymes, especially those with high thermal stability, have many uses in biotechnology. We have solved the crystal structure of a beta-1, 4-xylanase, XynB, from the extremely thermophilic bacterium Dictyoglomus thermophilum, isolate Rt46B.1. The protein crystallized from 1.6 M ammonium sulfate, 0.2 M HEPES pH 7.2 and 10% glycerol, with unit-cell parameters a = b = 91.3, c = 44.9 A and space group P4(3). The structure was solved at high resolution (1.8 A) by X-ray crystallography, using the method of isomorphous replacement with a single mercury derivative, and refined to a final R factor of 18.3% (R(free) = 22.1%). XynB has the single-domain fold typical of family 11 xylanases, comprising a jelly roll of two highly twisted beta-sheets that create a deep substrate-binding cleft. The two catalytic residues, Glu90 and Glu180, occupy this cleft. Compared with other family 11 xylanases, XynB has a greater proportion of polar surface and has a slightly extended C-terminus that, combined with the extension of beta-strand A5, gives additional hydrogen bonding and hydrophobic packing. These factors may account for the enhanced thermal stability of the enzyme.


    Related Citations: 
    • Crystallography & NMR system: A new software suite for macromolecular structure determination
      Brunger, A.T.,Adams, P.D.,Clore, G.M.,Delano, W.L.,Gros, P.,Grosse-Kunstleve, R.,Jiang, J.-S.,Kuszewski, J.,Nilges, M.,Pannu, N.S.,Read, R.J.,Rice, L.M.,Simonson, T.,Warren, G.
      (1998) Acta Crystallogr.,Sect.D 54: 905


    Organizational Affiliation

    School of Biological Sciences, University of Auckland, Private Bag 92-019, Auckland, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-1,4-XYLANASE
A, B
199Dictyoglomus thermophilumGene Names: xynB
EC: 3.2.1.8
Find proteins for P77853 (Dictyoglomus thermophilum)
Go to UniProtKB:  P77853
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 91.290α = 90.00
b = 91.290β = 90.00
c = 44.930γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance