9RTL | pdb_00009rtl

X-ray structure of the CTR107-N138A mutant bound to a tetramethylrhodamine ligand

• PDB DOI: https://doi.org/10.2210/pdb9RTL/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Chlorobaculum tepidum TLS
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-07-02 Released: 2025-07-30 
• Deposition Author(s): Tarnawski, M., Kompa, J., Johnsson, K.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of the CTR107-N138A mutant bound to a tetramethylrhodamine ligand

Tarnawski, M., Kompa, J., Johnsson, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.82 kDa 
• Atom Count: 2,554 
• Modeled Residue Count: 309 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AraC effector-binding domain-containing protein	A, B	160	Chlorobaculum tepidum TLS	Mutation(s): 1  Gene Names: CT0179
UniProt
Find proteins for Q8KFZ1 (Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS)) Explore Q8KFZ1  Go to UniProtKB:  Q8KFZ1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.81	α = 90
b = 71.81	β = 90
c = 146.16	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Tarnawski, M., Kompa, J., Johnsson, K.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release