9WO3 | pdb_00009wo3

E.coli beta-galactosidase in complex with fluorescent probe KSS9

• PDB DOI: https://doi.org/10.2210/pdb9WO3/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-09-06 Released: 2026-09-09 
• Deposition Author(s): Chen, X., Ge, Y.H., Yang, H., Wang, G.W., Guo, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.298 (Depositor) 
• R-Value Work: 
  0.270 (Depositor) 
• R-Value Observed: 
  0.271 (Depositor) 

Starting Model: experimental

wwPDB Validation

Currently 9WO3 does not have a validation slider image.

Literature

Identification of Senescence-Associated beta-Galactosidase With Single-Molecule Resolution

Wang, G., Chen, X., Ge, Y., Duan, K., Wu, S., Qiao, Q., Shi, D., Shen, J.W., Zhang, J., James, T.D., Xu, Z., Guo, Y.

(2026) Angew Chem Int Ed Engl n/a

• DOI: https://doi.org/10.1002/anie.5443283

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 467.81 kDa 
• Atom Count: 31,685 
• Modeled Residue Count: 4,080 
• Deposited Residue Count: 4,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase	A, B, C, D	1,025	Escherichia coli K-12	Mutation(s): 0  Gene Names: lacZ, b0344, JW0335 EC: 3.2.1.23
UniProt
Find proteins for P00722 (Escherichia coli (strain K12)) Explore P00722  Go to UniProtKB:  P00722

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EX2( Subject of Investigation/LOI)	G [auth C]	2-[7-(diethylamino)-2-[7-(diethylamino)-2-oxidanylidene-chromen-3-yl]chromenylium-4-yl]-~{N}-[4-[2-[(2~{R},3~{S},4~{R},5~{S},6~{S})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]sulfanylethylamino]-3-nitro-phenyl]sulfonyl-benzamide C47 H52 N5 O13 S2 BUHADKFLADGFSV-JANKNBMVSA-O
MG( Subject of Investigation/LOI)	E [auth A], F [auth B], H [auth C], I [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.298 (Depositor) 
• R-Value Work:  0.270 (Depositor) 
• R-Value Observed: 0.271 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 252.254	α = 90
b = 85.694	β = 93.76
c = 243.322	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Currently 9WO3 does not have a validation slider image.

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-09 
Deposition Author(s): Chen, X., Ge, Y.H., Yang, H., Wang, G.W., Guo, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22377098

Revision History  

• Version 1.0: 2026-09-09
  Type: Initial release