9J41 | pdb_00009j41

Crystal Structure of glucose tolerant beta-glucosidase UnBGl1 mutant (C188V)

PDB DOI: https://doi.org/10.2210/pdb9J41/pdb

Classification: HYDROLASE
Organism(s): soil metagenome
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.188 (Depositor), 0.199 (DCC)
R-Value Work:
0.168 (Depositor), 0.178 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 52.97 kDa
Atom Count: 4,250
Modeled Residue Count: 457
Deposited Residue Count: 477
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	477	soil metagenome	Mutation(s): 1 EC: 3.2.1.21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.188 (Depositor), 0.199 (DCC)
R-Value Work: 0.168 (Depositor), 0.178 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.88	α = 90
b = 66.27	β = 90
c = 138.25	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Suryawanshi, A.B.

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.