Crystal structure of the extracellular xylanase from Geobacillus stearothermophilus T-6 (XT6, monoclinic form): The complex of the WT enzyme with xylopentaose at 1.67A resolution

Experimental Data Snapshot

  • Resolution: 1.67 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

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This is version 2.1 of the entry. See complete history


Mapping glycoside hydrolase substrate subsites by isothermal titration calorimetry.

Zolotnitsky, G.Cogan, U.Adir, N.Solomon, V.Shoham, G.Shoham, Y.

(2004) Proc Natl Acad Sci U S A 101: 11275-11280

  • DOI: https://doi.org/10.1073/pnas.0404311101
  • Primary Citation of Related Structures:  
    1R85, 1R87

  • PubMed Abstract: 

    Relating thermodynamic parameters to structural and biochemical data allows a better understanding of substrate binding and its contribution to catalysis. The analysis of the binding of carbohydrates to proteins or enzymes is a special challenge because of the multiple interactions and forces involved. Isothermal titration calorimetry (ITC) provides a direct measure of binding enthalpy (DeltaHa) and allows the determination of the binding constant (free energy), entropy, and stoichiometry. In this study, we used ITC to elucidate the binding thermodynamics of xylosaccharides for two xylanases of family 10 isolated from Geobacillus stearothermophilus T-6. The change in the heat capacity of binding (DeltaCp = DeltaH/DeltaT) for xylosaccharides differing in one sugar unit was determined by using ITC measurements at different temperatures. Because hydrophobic stacking interactions are associated with negative DeltaCp, the data allow us to predict the substrate binding preference in the binding subsites based on the crystal structure of the enzyme. The proposed positional binding preference was consistent with mutants lacking aromatic binding residues at different subsites and was also supported by tryptophan fluorescence analysis.

  • Organizational Affiliation

    Department of Biotechnology, Technion-Israel Institute of Technology, Haifa 32000, Israel.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase379Geobacillus stearothermophilusMutation(s): 0 
Gene Names: xynA
Find proteins for P40943 (Geobacillus stearothermophilus)
Explore P40943 
Go to UniProtKB:  P40943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40943
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G87728WL
GlyCosmos:  G87728WL
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G87429QT
GlyCosmos:  G87429QT
Biologically Interesting Molecules (External Reference) 2 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.67 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.422α = 90
b = 61.221β = 119.5
c = 89.583γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model, Non-polymer description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary