9LFS | pdb_00009lfs

Crystal of Glucosidase form Ophiorrhiza pumila

PDB DOI: https://doi.org/10.2210/pdb9LFS/pdb

Classification: PLANT PROTEIN
Organism(s): Ophiorrhiza pumila
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-08 Released: 2026-01-14
Deposition Author(s): Hao, X.L., Kai, G.Y.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.203 (Depositor), 0.204 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal of Glucosidase form Ophiorrhiza pumila

Hao, X.L., Kai, G.Y.

To be published.

Macromolecule Content

Total Structure Weight: 62.08 kDa
Atom Count: 4,118
Modeled Residue Count: 469
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OpBGlu1	A	540	Ophiorrhiza pumila	Mutation(s): 0
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
A1ELV (Subject of Investigation/LOI) Query on A1ELV Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	Loganin C₁₇ H₂₆ O₁₀ AMBQHHVBBHTQBF-UOUCRYGSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.203 (Depositor), 0.204 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.755	α = 90
b = 137.755	β = 90
c = 164.896	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2026-01-14

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	2023YFC3503900

Revision History (Full details and data files)

Version 1.0: 2026-01-14
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.