9RTM | pdb_00009rtm

X-ray structure of the rhodamine-binding protein tag (Rho-tag) bound to a tetramethylrhodamine ligand

PDB DOI: https://doi.org/10.2210/pdb9RTM/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: 2.10 Å
R-Value Free:
0.216 (Depositor), 0.229 (DCC)
R-Value Work:
0.195 (Depositor), 0.198 (DCC)
R-Value Observed:
0.220 (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 rhodamine-binding protein tag (Rho-tag) bound to a tetramethylrhodamine ligand

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

To be published.

Macromolecule Content

Total Structure Weight: 35.47 kDa
Atom Count: 2,466
Modeled Residue Count: 309
Deposited Residue Count: 316
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	158	Chlorobaculum tepidum TLS	Mutation(s): 19 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 1 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 D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [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 D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.216 (Depositor), 0.229 (DCC)
R-Value Work: 0.195 (Depositor), 0.198 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.09	α = 90
b = 62.35	β = 90
c = 96.79	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2025-07-30
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.