9NT6 | pdb_00009nt6

Crystal structure of ecLacI transcription factor ancestor 4 bound to Beta-methyl-D-galactoside

• PDB DOI: https://doi.org/10.2210/pdb9NT6/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-18 Released: 2025-06-18 
• Deposition Author(s): Georgelin, R.L., Frkic, R.L., Tan, L., Kaczmarski, J., Jackson, C.J.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ecLacI transcription factor ancestor 4 bound to Beta-methyl-D-galactoside

Georgelin, R.L., Frkic, R.L., Tan, L., Kaczmarski, J., Jackson, C.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.97 kDa 
• Atom Count: 4,746 
• Modeled Residue Count: 548 
• Deposited Residue Count: 562 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LacI Transcription Factor	A, B	281	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for B8LFD5 (Escherichia coli (strain K12)) Explore B8LFD5  Go to UniProtKB:  B8LFD5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBG (Subject of Investigation/LOI)	C [auth A], F [auth B]	methyl beta-D-galactopyranoside C7 H14 O6 HOVAGTYPODGVJG-VOQCIKJUSA-N
EDO	D [auth A], E [auth A], G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.208 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.467	α = 90
b = 108.336	β = 90
c = 119.601	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-18 
Deposition Author(s): Georgelin, R.L., Frkic, R.L., Tan, L., Kaczmarski, J., Jackson, C.J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE200100012
Australian Research Council (ARC)	Australia	CE200100029

Revision History  

• Version 1.0: 2025-06-18
  Type: Initial release