Crystal structure of the Pseudomonas putida Xre-RES toxin-antitoxin complex bound to promoter DNA

entry_id	9r35
deposition_date	2025-05-02
title	Crystal structure of the Pseudomonas putida Xre-RES toxin-antitoxin complex bound to promoter DNA
keywords	Protein-DNA complex, RES toxin, Xre antitoxin, GENE REGULATION; GENE REGULATION
method	X-RAY DIFFRACTION

rg_guinier	56.83 Å
rg_electron	57.04 Å
i0	3314310000.00
molecular_weight	449870.0 kDa
excluded_volume	549440 ų
envelope_volume	827080 ų
shell_volume	120840 ų
envelope_diameter	198.4 Å
shell_rg	60.79 Å
envelope_rg	54.74 Å
shape_rg	57.07 Å
total_rg	57.03 Å
total_atoms	31452
n_residues	3700
n_harmonics	20
q_range	— – 0.5000 Å−1
n_points	101
shell_type	directional
solvent_density	0.3340 e/ų
contrast_shell	0.0300 e/ų
crysol_version	4.1.3

dmax	181.1 Å
rg_real	56.75 Å
rg_real_error	1.68 Å
i0_real	3.3140e+09
i0_real_error	6.2000e+07
rg_reciprocal	56.89 Å
i0_reciprocal	3315000000.0000
total_estimate	0.8167
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	64.7 Å
skewness	0.323
kurtosis	-0.240
angular_range	— – 0.1400 Å−1
current_alpha	0.0000
highest_alpha	149800000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

Unit Cell

length_a	81.230 Å
length_b	185.110 Å
length_c	170.790 Å
angle_alpha	90.00 °
angle_beta	90.01 °
angle_gamma	90.00 °
z_pdb	32

Symmetry

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

Refinement

resolution	2.700 Å
resolution_low	26.030 Å
r_factor	—
r_work	0.2280
r_free	0.2690

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/r3/9r35/pr_distribution.json
• pr_output /app/data/pr_computation/r3/9r35/9r35.pr.out
• pr_plot /app/data/visualization/pr_computation/r3/9r35/9r35_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/r3/9r35/9r35.dat
• saxs_fit /app/data/saxs_computation/r3/9r35/9r35.fit
• saxs_log /app/data/saxs_computation/r3/9r35/9r35.log
• saxs_plot /app/data/visualization/saxs_computation/r3/9r35/9r35_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/r3/9r35/9r35.fit
pddf	/app/data/pr_computation/r3/9r35/9r35.pr.out
profile	/app/data/saxs_computation/r3/9r35/9r35.dat