Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 44.33 kDa 
• Atom Count: 3730 
• Modelled Residue Count: 375 
• Deposited Residue Count: 379 
• Unique protein chains: 1

1HIZ

Xylanase T6 (Xt6) from Bacillus Stearothermophilus

• PDB DOI: 10.2210/pdb1HIZ/pdb

• Classification: GLYCOSIDASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-01-05 Released: 2002-01-04 
• Deposition Author(s): Sainz, G., Tepplitsky, A., Stojanoff, V., Thompson, A., Shoham, Y., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.188 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Literature

Structure Determination of the Extracellular Xylanase from Geobacillus Stearothermophilus by Selenomethionyl MAD Phasing

Teplitsky, A., Mechaly, A., Stojanoff, V., Sainz, G., Golan, G., Feinberg, H., Gilboa, R., Reiland, V., Zolotnitsky, G., Shallom, D., Thompson, A., Shoham, Y., Shoham, G.

(2004) Acta Crystallogr D Biol Crystallogr 60: 836

• PubMed: 15103129 
• DOI: 10.1107/S0907444904004123
• Primary Citation of Related Structures:  
  1HIZ


• PubMed Abstract: 
  

Xylanases are hemicellulases that hydrolyze the internal beta-1,4-glycoside bonds of xylan. The extracellular thermostable endo-1,4-beta-xylanase (EC 3.2.1.8; XT6) produced by the thermophilic bacterium Geobacillus stearothermophilus T-6 was shown to bleach pulp optimally at pH 9 and 338 K and was successfully used in a large-scale biobleaching mill trial. The xylanase gene was cloned and sequenced. The mature enzyme consists of 379 amino acids, with a calculated molecular weight of 43 808 Da and a pI of 9.0. Crystallographic studies of XT6 were performed in order to study the mechanism of catalysis and to provide a structural basis for the rational introduction of enhanced thermostability by site-specific mutagenesis. XT6 was crystallized in the primitive trigonal space group P3(2)21, with unit-cell parameters a = b = 112.9, c = 122.7 A. A full diffraction data set for wild-type XT6 has been measured to 2.4 A resolution on flash-frozen crystals using synchrotron radiation. A fully exchanged selenomethionyl XT6 derivative (containing eight Se atoms per XT6 molecule) was also prepared and crystallized in an isomorphous crystal form, providing full selenium MAD data at three wavelengths and enabling phase solution and structure determination. The structure of wild-type XT6 was refined at 2.4 A resolution to a final R factor of 15.6% and an R(free) of 18.6%. The structure demonstrates that XT6 is made up of an eightfold TIM-barrel containing a deep active-site groove, consistent with its 'endo' mode of action. The two essential catalytic carboxylic residues (Glu159 and Glu265) are located at the active site within 5.5 A of each other, as expected for 'retaining' glycoside hydrolases. A unique subdomain was identified in the carboxy-terminal part of the enzyme and was suggested to have a role in xylan binding. The three-dimensional structure of XT6 is of great interest since it provides a favourable starting point for the rational improvement of its already high thermal and pH stabilities, which are required for a number of biotechnological and industrial applications.

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Organizational Affiliation: 

Department of Inorganic Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE	A	379	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: XYNA EC: 3.2.1.8
UniProt
Find proteins for P40943 (Geobacillus stearothermophilus) Explore P40943  Go to UniProtKB:  P40943

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	C [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
GLA	B [auth A]	alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.188 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.87	α = 90
b = 112.87	β = 90
c = 122.73	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-01-05 
• Released Date: 2002-01-04 
Deposition Author(s): Sainz, G., Tepplitsky, A., Stojanoff, V., Thompson, A., Shoham, Y., Shoham, G.

Revision History  

• Version 1.0: 2002-01-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary