9JLZ | pdb_00009jlz

High resolution crystal structure of GH1 beta-glucosidase from soil metagenome (UnBGl1)

PDB DOI: https://doi.org/10.2210/pdb9JLZ/pdb

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

Deposited: 2024-09-20 Released: 2026-02-04
Deposition Author(s): Suryawanshi, A.B., Bhaumik, P.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.147 (Depositor), 0.148 (DCC)
R-Value Work:
0.126 (Depositor), 0.127 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9JLZ

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: 53.28 kDa
Atom Count: 4,383
Modeled Residue Count: 457
Deposited Residue Count: 477
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.147 (Depositor), 0.148 (DCC)
R-Value Work: 0.126 (Depositor), 0.127 (DCC)
R-Value Observed: 0.127 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.84	α = 90
b = 65.99	β = 90
c = 138.18	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.