Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.94 kDa 
• Atom Count: 2764 
• Residue Count: 313 
• Unique protein chains: 1

3WUB

The wild type crystal structure of b-1,4-Xylanase (XynAS9) from Streptomyces sp. 9

• DOI: 10.2210/pdb3WUB/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces sp.
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2014-04-23 Released: 2014-10-29 
• Deposition Author(s): Chen, C.C., Han, X., Lv, P., Ko, T.P., Peng, W., Huang, C.H., Zheng, Y., Gao, J., Yang, Y.Y., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.221 
• R-Value Work: 0.196 

Literature

Structural perspectives of an engineered beta-1,4-xylanase with enhanced thermostability.

Chen, C.C., Luo, H., Han, X., Lv, P., Ko, T.P., Peng, W., Huang, C.H., Wang, K., Gao, J., Zheng, Y., Yang, Y., Zhang, J., Yao, B., Guo, R.T.

(2014) J Biotechnol 189C: 175-182

• PubMed: 25193708 
• DOI: 10.1016/j.jbiotec.2014.08.030
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The glycoside hydrolase 10 (GH10) xylanase from Streptomyces sp. 9 (XynAS9) can operate in a broad range of pH and temperature, and thus is a potential candidate for commercial applications. Recently, we engineered XynAS9 via mutating several residues in accordance with the consensus sequences of GH10 thermophilic xylanases in an attempt to improve the enzyme thermostability and thermotolerance. The most promising effects were observed in the double mutant V81P/G82E. In order to investigate the molecular mechanism of the improved thermal profile of XynAS9, complex crystal structures of the wild type (WT) and mutant (MT) enzyme were solved at 1.88-2.05Å resolution. The structures reveal a classical GH10 (β/α)8 TIM-barrel fold. In MT XynAS9, E82 forms several interactions to its neighboring residues, which might aid in stabilizing the local structure. Furthermore, the MT structure showed lower B factors for individual residues compared to the WT structure, reflecting the increased MT protein rigidity. Analyses of the XynAS9 structures also delineate the detailed enzyme-substrate interaction network. More importantly, possible explanations for the enhanced thermal profiles of MT XynAS9 are proposed, which may be a useful strategy for enzyme engineering in the future.

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Organizational Affiliation: 

Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Endo-1,4-beta-xylanase A	A	313	Streptomyces sp.	Mutation(s): 0  Gene Names: xynAS9 EC: 3.2.1.8
Find proteins for B4XVN1 (Streptomyces sp) Go to UniProtKB:  B4XVN1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 0.221 
• R-Value Work: 0.196 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.91	α = 90
b = 80.91	β = 90
c = 289.302	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-23 
• Released Date: 2014-10-29 
Deposition Author(s): Chen, C.C., Han, X., Lv, P., Ko, T.P., Peng, W., Huang, C.H., Zheng, Y., Gao, J., Yang, Y.Y., Guo, R.T.

Revision History 

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection