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: 46.61 kDa 
• Atom Count: 3,959 
• Modelled Residue Count: 414 
• Deposited Residue Count: 414 
• Unique protein chains: 1

 1QH7

CATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,5B CONFORMATION FOR THE GLYCOSYL-ENZYME INTERMIDIATE REVEALED BY THE STRUCTURE OF THE BACILLUS AGARADHAERENS FAMILY 11 XYLANASE

• PDB DOI: 10.2210/pdb1QH7/pdb

• Classification: HYDROLASE
• Organism(s): Salipaludibacillus agaradhaerens
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 1999-05-11 Released: 2000-05-17 
• Deposition Author(s): Sabini, E., Sulzenbacher, G., Dauter, M., Dauter, Z., Jorgensen, P.L., Schulein, M., Dupont, C., Davies, G.J., Wilson, K.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.176 
• R-Value Work: 0.117 

Literature

Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5B conformation for the glycosyl-enzyme intermediate revealed by the structure of the Bacillus agaradhaerens family 11 xylanase.

Sabini, E., Sulzenbacher, G., Dauter, M., Dauter, Z., Jorgensen, P.L., Schulein, M., Dupont, C., Davies, G.J., Wilson, K.S.

(1999) Chem Biol 6: 483-492

• PubMed: 10381409 
• DOI: 10.1016/s1074-5521(99)80066-0
• Primary Citation of Related Structures:  
  1H4G, 1H4H, 1QH6, 1QH7


• PubMed Abstract: 
  

The enzymatic hydrolysis of glycosides involves the formation and subsequent breakdown of a covalent glycosyl-enzyme intermediate via oxocarbenium-ion-like transition states. The covalent intermediate may be trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details of the intermediate conformation and noncovalent interactions between enzyme and oligosaccharide. Xylanases are important in industrial applications - in the pulp and paper industry, pretreating wood with xylanases decreases the amount of chlorine-containing chemicals used. Xylanases are structurally similar to cellulases but differ in their specificity for xylose-based, versus glucose-based, substrates.

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Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, Y010 5DD, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XYLANASE	A, B	207	Salipaludibacillus agaradhaerens	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for Q7SIE3 (Salipaludibacillus agaradhaerens) Explore Q7SIE3  Go to UniProtKB:  Q7SIE3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYP	C [auth A], D [auth B]	beta-D-xylopyranose C5 H10 O5 SRBFZHDQGSBBOR-KKQCNMDGSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.176 
• R-Value Work: 0.117 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.86	α = 90
b = 75.36	β = 90
c = 78.4	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-17 
Deposition Author(s): Sabini, E., Sulzenbacher, G., Dauter, M., Dauter, Z., Jorgensen, P.L., Schulein, M., Dupont, C., Davies, G.J., Wilson, K.S.

Revision History  

• Version 1.0: 2000-05-17
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-12-25
  Changes: Database references, Derived calculations, Polymer sequence
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary