9J4Q | pdb_00009j4q

Crystal structure of glucose bound covalent intermediate of GH1 beta-glucosidase (UnBGl1)

• PDB DOI: https://doi.org/10.2210/pdb9J4Q/pdb

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


• Deposited: 2024-08-09 Released: 2026-02-04 
• Deposition Author(s): Suryawanshi, A.B., Bhaumik, P.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.232 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Rewiring Catalytic Craters: A Path for Engineering beta-Glucosidases to Improve Glucose Tolerance

Suryawanshi, A.B., Bedi, R.K., Pawar, M., Noronha, S., Bhaumik, P.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.01.02.631061

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 53.57 kDa 
• Atom Count: 3,853 
• Modeled Residue Count: 457 
• Deposited Residue Count: 477 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	477	soil metagenome	Mutation(s): 0  EC: 3.2.1.21

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.232 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.2	α = 90
b = 65.8	β = 90
c = 137.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Suryawanshi, A.B., Bhaumik, P.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	BT/PR41982/PBD/26/822/2021

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release