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

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
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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

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

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

To be published.

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

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KFZ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EI4 (Subject of Investigation/LOI) Query on A1EI4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	[9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium C₂₄ H₂₃ N₂ O₃ ABZLKHKQJHEPAX-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B]