9L0N | pdb_00009l0n

The crystal structure of the beta-glucosidase Ks5A7

PDB DOI: https://doi.org/10.2210/pdb9L0N/pdb

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

Deposited: 2024-12-12 Released: 2025-10-15
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: 2.50 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.216 (Depositor), 0.215 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of the beta-glucosidase Ks5A7

Xie, W., Yang, N.

To be published.

Macromolecule Content

Total Structure Weight: 214.83 kDa
Atom Count: 15,722
Modeled Residue Count: 1,815
Deposited Residue Count: 1,840
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase Ks5A7	A, B, C, D	460	metagenome	Mutation(s): 0 EC: 3.2.1.21
UniProt
Find proteins for A0AA42DMU7 (Holtiella tumoricola) Explore A0AA42DMU7 Go to UniProtKB: A0AA42DMU7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0AA42DMU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth D] SDF format, chain E [auth B] MOL2 format, chain F [auth D] MOL2 format, chain E [auth B] mmCIF format, chain F [auth D] mmCIF format, chain E [auth B]	E [auth B], F [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.216 (Depositor), 0.215 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.037	α = 90
b = 112.936	β = 101.227
c = 99.389	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-15
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.