1I1W

0.89A Ultra high resolution structure of a Thermostable Xylanase from Thermoascus Aurantiacus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.090 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy.

Natesh, R.Manikandan, K.Bhanumoorthy, P.Viswamitra, M.A.Ramakumar, S.

(2003) Acta Crystallogr.,Sect.D 59: 105-117

  • Primary Citation of Related Structures:  1I1X

  • PubMed Abstract: 
  • Thermoascus aurantiacus xylanase is a thermostable enzyme which hydrolyses xylan, a major hemicellulose component of the biosphere. The crystal structure of this F/10 family xylanase, which has a triosephosphate isomerase (TIM) barrel (beta/alpha)(8) ...

    Thermoascus aurantiacus xylanase is a thermostable enzyme which hydrolyses xylan, a major hemicellulose component of the biosphere. The crystal structure of this F/10 family xylanase, which has a triosephosphate isomerase (TIM) barrel (beta/alpha)(8) fold, has been solved to small-molecule accuracy at atomic resolution (1.11 A) at 293 K (RTUX) and at ultrahigh resolution (0.89 A) at 100 K (CTUX) using X-ray diffraction data sets collected on a synchrotron light source, resulting in R/R(free) values of 9.94/12.36 and 9.00/10.61% (for all data), respectively. Both structures were refined with anisotropic atomic displacement parameters. The 0.89 A structure, with 177 476 observed unique reflections, was refined without any stereochemical restraints during the final stages. The salt bridge between Arg124 and Glu232, which is bidentate in RTUX, is water-mediated in CTUX, suggesting the possibility of plasticity of ion pairs in proteins, with water molecules mediating some of the alternate arrangements. Two buried waters present inside the barrel form hydrogen-bond interactions with residues in strands beta2, beta3, beta4 and beta7 and presumably contribute to structural stability. The availability of accurate structural information at two different temperatures enabled the study of the temperature-dependent deformations of the TIM-barrel fold of the xylanase. Analysis of the deviation of corresponding C(alpha) atoms between RTUX and CTUX suggests that the interior beta-strands are less susceptible to changes as a function of temperature than are the alpha-helices, which are on the outside of the barrel. betaalpha-loops, which are longer and contribute residues to the active-site region, are more flexible than alphabeta-loops. The 0.89 A structure represents one of the highest resolution structures of a protein of such size with one monomer molecule in the asymmetric unit and also represents the highest resolution TIM-barrel fold structure to date. It may provide a useful template for theoretical modelling studies of the structure and dynamics of the ubiquitous TIM-barrel fold.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Crystals of Thermoascus Aurantiacus Xylanase
      Viswamitra, M.A.,Bhanumoorthy, P.,Ramakumar, S.,Manjula, M.V.,Vithayathil, P.J.,Murthy, S.K.,Naren, A.P.
      (1993) J.Mol.Biol. 232: 987
    • Crystal Structure at 1.8 A Resolution and Proposed Amino Acid Sequence of a Thermostable Xylanase from Thermoascus Aurantiascus
      Natesh, R.,Bhanumoorthy, P.,Vithayathil, P.J.,Sekar, K.,Ramakumar, S.,Viswamitra, M.A.
      (1999) J.Mol.Biol. 288: 999


    Organizational Affiliation

    Department of Physics, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENDO-1,4-BETA-XYLANASE
A
303Thermoascus aurantiacusGene Names: XYNA
EC: 3.2.1.8
Find proteins for P23360 (Thermoascus aurantiacus)
Go to UniProtKB:  P23360
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACN
Query on ACN

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A
ACETONE
C3 H6 O
CSCPPACGZOOCGX-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
EOH
Query on EOH

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Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.89 Å
  • R-Value Free: 0.106 
  • R-Value Work: 0.090 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.050α = 90.00
b = 66.990β = 113.50
c = 50.760γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXL-97refinement
SCALEPACKdata scaling
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Version format compliance
  • Version 1.3: 2014-06-04
    Type: Non-polymer description