9L0Q | pdb_00009l0q

The crystal structure of the beta-glucosidase Ks5A7

• PDB DOI: https://doi.org/10.2210/pdb9L0Q/pdb

• Classification: HYDROLASE
• Organism(s): metagenome
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-12 Released: 2025-06-18 
• Deposition Author(s): Xie, W., Yang, N.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Rational design on the beta-glucosidase Ks5A7 reveals a hidden site for improved enzymatic performance

Yang, N., Liu, A., Lu, H., Yang, X., Wu, X., Cao, L., Jiang, S., Xie, W.

(2025) Food Biosci 68: 106691

• DOI: https://doi.org/10.1016/j.fbio.2025.106691

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 107.29 kDa 
• Atom Count: 8,032 
• Modeled Residue Count: 909 
• Deposited Residue Count: 920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase Ks5A7	A, B	460	metagenome	Mutation(s): 0  EC: 3.2.1.21
UniProt
Find proteins for A0AA42DMU7 (Holtiella tumoricola) Explore A0AA42DMU7  Go to UniProtKB:  A0AA42DMU7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.121	α = 90
b = 83.886	β = 90.42
c = 145.551	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Xie, W., Yang, N.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32271322

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release