3ZSE

3D Structure of a thermophilic family GH11 xylanase from Thermobifida fusca

• PDB DOI: https://doi.org/10.2210/pdb3ZSE/pdb

• Classification: HYDROLASE
• Organism(s): Thermobifida fusca
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2011-06-27 Released: 2012-02-08 
• Deposition Author(s): Lammerts van Bueren, A., Otani, S., Friis, E.P., S Wilson, K., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Three-Dimensional Structure of a Thermophilic Family Gh11 Xylanase from Thermobifida Fusca.

Lammerts Van Bueren, A., Otani, S., Friis, E.P., Wilson, K.S., Davies, G.J.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 141

• PubMed: 22297985 
• DOI: https://doi.org/10.1107/S1744309111049608
• Primary Citation of Related Structures:  
  3ZSE


• PubMed Abstract: 
  

  Thermostable enzymes employ various structural features dictated at the amino-acid sequence level that allow them to maintain their integrity at higher temperatures. Many hypotheses as to the nature of thermal stability have been proposed, including optimized core hydrophobicity and an increase in charged surface residues to enhance polar solvent interactions for solubility. Here, the three-dimensional structure of the family GH11 xylanase from the moderate thermophile Thermobifida fusca in its trapped covalent glycosyl-enzyme intermediate complex is presented. Interactions with the bound ligand show fewer direct hydrogen bonds from ligand to protein than observed in previous complexes from other species and imply that binding of the xylan substrate involves several water-mediated hydrogen bonds.

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Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, University of York, York, England.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.85 kDa 
• Atom Count: 1,663 
• Modelled Residue Count: 188 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDO-1,4-BETA-XYLANASE	A	201	Thermobifida fusca	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for Q5RZ98 (Thermobifida fusca) Explore Q5RZ98  Go to UniProtKB:  Q5RZ98

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-xylopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G53360CN GlyCosmos:  G53360CN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.241 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.63	α = 90
b = 41.31	β = 90
c = 93.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-08 
Deposition Author(s): Lammerts van Bueren, A., Otani, S., Friis, E.P., S Wilson, K., Davies, G.J.

Revision History  

• Version 1.0: 2012-02-08
  Type: Initial release
  
• Version 1.1: 2012-03-28
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary