9LPX | pdb_00009lpx

X-ray structure of GH1 beta-glucosidase Td2F2 2F-Glc complex at room temperature

• PDB DOI: https://doi.org/10.2210/pdb9LPX/pdb

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


• Deposited: 2025-01-26 Released: 2025-10-29 
• Deposition Author(s): Yano, N., Arakawa, H., Lin, C.C., Ishiwata, A., Tanaka, K., Kusaka, K., Fushinobu, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 
  0.168 (Depositor), 0.167 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Neutron crystallography of the covalent intermediate of beta-glucosidase reveals remodeling of the catalytic center.

Yano, N., Arakawa, H., Lin, C.C., Ishiwata, A., Tanaka, K., Kusaka, K., Fushinobu, S.

(2025) Proc Natl Acad Sci U S A 

• DOI: https://doi.org/10.1073/pnas.2502828122

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.24 kDa 
• Atom Count: 3,859 
• Modeled Residue Count: 440 
• Deposited Residue Count: 457 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE	A	457	metagenome	Mutation(s): 0  EC: 3.2.1.21

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE (Subject of Investigation/LOI)	C [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
G2F (Subject of Investigation/LOI)	B [auth A]	2-deoxy-2-fluoro-alpha-D-glucopyranose C6 H11 F O5 ZCXUVYAZINUVJD-UKFBFLRUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free:  0.168 (Depositor), 0.167 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.54	α = 90
b = 71.23	β = 90
c = 97.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Yano, N., Arakawa, H., Lin, C.C., Ishiwata, A., Tanaka, K., Kusaka, K., Fushinobu, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	22K06157
Japan Society for the Promotion of Science (JSPS)	Japan	19H00929
Japan Society for the Promotion of Science (JSPS)	Japan	24H02269

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release