1NP2

Crystal structure of thermostable beta-glycosidase from thermophilic eubacterium Thermus nonproteolyticus HG102

• PDB DOI: https://doi.org/10.2210/pdb1NP2/pdb

• Classification: HYDROLASE
• Organism(s): Thermus nonproteolyticus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-01-16 Released: 2003-07-15 
• Deposition Author(s): Liang, D.C., Chang, W.R., Wang, X.Q., He, X.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.272 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 

Starting Model: experimental

Literature

Structural Basis for Thermostability of beta-Glycosidase from the Thermophilic Eubacterium Thermus nonproteolyticus HG102.

Wang, X., He, X., Yang, S., An, X., Chang, W., Liang, D.

(2003) J Bacteriol 185: 4248-4255

• PubMed: 12837801 
• DOI: https://doi.org/10.1128/JB.185.14.4248-4255.2003
• Primary Citation of Related Structures:  
  1NP2


• PubMed Abstract: 
  

  The three-dimensional structure of a thermostable beta-glycosidase (Gly(Tn)) from the thermophilic eubacterium Thermus nonproteolyticus HG102 was determined at a resolution of 2.4 A. The core of the structure adopts the (betaalpha)(8) barrel fold. The sequence alignments and the positions of the two Glu residues in the active center indicate that Gly(Tn) belongs to the glycosyl hydrolases of retaining family 1. We have analyzed the structural features of Gly(Tn) related to the thermostability and compared its structure with those of other mesophilic glycosidases from plants, eubacteria, and hyperthermophilic enzymes from archaea. Several possible features contributing to the thermostability of Gly(Tn) were elucidated.

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Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

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: 98.11 kDa 
• Atom Count: 7,156 
• Modelled Residue Count: 852 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-glycosidase	A, B	436	Thermus nonproteolyticus	Mutation(s): 0  EC: 3.2.1.21
UniProt
Find proteins for Q9L794 (Thermus nonproteolyticus) Explore Q9L794  Go to UniProtKB:  Q9L794

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.272 
• R-Value Work: 0.230 
• R-Value Observed: 0.230 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.7	α = 90
b = 94.755	β = 90
c = 176.72	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: 2003-07-15 
Deposition Author(s): Liang, D.C., Chang, W.R., Wang, X.Q., He, X.Y.

Revision History  

• Version 1.0: 2003-07-15
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description