9NT5 | pdb_00009nt5

Crystal structure of ecLacI transcription factor ancestor 1 bound to glycerol

PDB DOI: https://doi.org/10.2210/pdb9NT5/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.212 (Depositor), 0.212 (DCC)
R-Value Work:
0.189 (Depositor), 0.188 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of ecLacI transcription factor ancestor 1 bound to glycerol

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

To be published.

Macromolecule Content

Total Structure Weight: 30.79 kDa
Atom Count: 2,244
Modeled Residue Count: 270
Deposited Residue Count: 280
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LacI Transcription Factor	A	280	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.212 (Depositor), 0.212 (DCC)
R-Value Work: 0.189 (Depositor), 0.188 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.821	α = 90
b = 104.821	β = 90
c = 50.126	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Georgelin, R.L.

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

Revision History (Full details and data files)

Version 1.0: 2025-06-18
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.