1IGO | pdb_00001igo

Family 11 xylanase

• PDB DOI: https://doi.org/10.2210/pdb1IGO/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Mutation(s): No 


• Deposited: 2001-04-18 Released: 2002-04-18 
• Deposition Author(s): Oakley, A.J., Thomson, C., Heinrich, T., Dunlop, R., Wilce, M.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching.

Oakley, A.J., Heinrich, T., Thompson, C.A., Wilce, M.C.

(2003) Acta Crystallogr D Biol Crystallogr 59: 627-636

• PubMed: 12657781 
• DOI: https://doi.org/10.1107/s0907444903001227
• Primary Citation Related Structures: 
  1IGO


• PubMed Abstract: 
  

  Enzymes such as family 11 xylanases are increasingly being used for industrial applications. Here, the cloning, structure determination and temperature-stability data of a family 11 xylanase, Xyn11X, from the alkali-tolerant Bacillus subtilis subspecies B230 are reported. This enzyme, which degrades xylan polymers, is being produced on an industrial scale for use in the paper-bleaching industry. Xyn11X adopts the canonical family 11 xylanase fold. It has a greater abundance of side chain to side chain hydrogen bonds compared with all other family 11 xylanase crystal structures. Means by which the thermostability of Xyn11X might be improved are suggested.

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Organizational Affiliation: 
• School of Biomedical and Chemical Sciences, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Australia.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 45.26 kDa 
• Atom Count: 3,300 
• Modeled Residue Count: 410 
• Deposited Residue Count: 410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
family 11 xylanase	A, B	205	Bacillus subtilis	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for Q7SID8 (Bacillus subtilis) Explore Q7SID8  Go to UniProtKB:  Q7SID8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.19	α = 90
b = 52.54	β = 97.83
c = 65.41	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-04-18 
Deposition Author(s): Oakley, A.J., Thomson, C., Heinrich, T., Dunlop, R., Wilce, M.C.J.

Revision History  

• Version 1.0: 2002-04-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description