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9rtl

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

Method: X-RAY DIFFRACTION D_max: 71.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rtl
deposition_date	2025-07-02
last_revision	2025-07-30
title	X-ray structure of the CTR107-N138A mutant bound to a tetramethylrhodamine ligand
keywords	Rhodamine-binding protein, Rho-tag, Tetramethylrhodamine, UNKNOWN FUNCTION; UNKNOWN FUNCTION
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	20.64 Å
rg_electron	19.85 Å
i0	36871900.00
molecular_weight	32098.0 kDa
excluded_volume	31455 Å³
envelope_volume	50079 Å³
shell_volume	21147 Å³
envelope_diameter	71.9 Å
shell_rg	26.28 Å
envelope_rg	20.10 Å
shape_rg	19.82 Å
total_rg	20.55 Å
total_atoms	2431
n_residues	309
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	71.8 Å
rg_real	20.58 Å
rg_real_error	0.47 Å
i0_real	3.6870e+07
i0_real_error	5.0760e+05
rg_reciprocal	20.59 Å
i0_reciprocal	36870000.0000
total_estimate	0.8640
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.7 Å
skewness	0.286
kurtosis	-0.289
angular_range	— – 0.3850 Å⁻¹
current_alpha	0.0000
highest_alpha	8389000.0000
n_real_points	70
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.749; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	AraC effector-binding domain-containing protein
formula_weight	17294.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2554

MDFECQFVCELKELAPVPALLIRTQTTMSELGSLFEAGYHDILQLLAGQGKSPSGPPFARYFGMSAGTFEVEFGFPVEGGVEGSGRVVTGLTPSGKAASSLYIGPYGEIEAVYDALMKWVDDNGFDLSGEAYEIYLDAPAETAPDQLRTRVSLMLHESLE

Source

organism	Chlorobaculum tepidum TLS
ncbi_taxonomy_id	194439
host_organism	Escherichia coli

Entity 2 non-polymer

description	[9-(2-carboxyphenyl)-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium
formula_weight	387.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	123

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6. Citations (1)

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length_a	71.810 Å
length_b	71.810 Å
length_c	146.160 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65
int_tables_number	170
crystal_system	hexagonal

resolution	1.800 Å
resolution_low	38.350 Å
r_factor	0.1840
r_work	0.1825
r_free	0.2133

fit	/app/data/saxs_computation/rt/9rtl/9rtl.fit
pddf	/app/data/pr_computation/rt/9rtl/9rtl.pr.out
profile	/app/data/saxs_computation/rt/9rtl/9rtl.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction