Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode II

entry_id	9y0q
deposition_date	2025-08-28
title	Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode II
keywords	Thiol oxidase mutant, bacterial foldase, thioredoxin fold, complex, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

rg_guinier	18.11 Å
rg_electron	16.88 Å
i0	8941530.00
molecular_weight	22287.0 kDa
excluded_volume	28011 ų
envelope_volume	32196 ų
shell_volume	16127 ų
envelope_diameter	60.4 Å
shell_rg	22.68 Å
envelope_rg	17.14 Å
shape_rg	16.86 Å
total_rg	17.91 Å
total_atoms	1576
n_residues	200
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	61.4 Å
rg_real	18.03 Å
rg_real_error	0.39 Å
i0_real	8.9420e+06
i0_real_error	1.0600e+05
rg_reciprocal	18.04 Å
i0_reciprocal	8942000.0000
total_estimate	0.8682
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.4 Å
skewness	0.250
kurtosis	-0.328
angular_range	— – 0.4400 Å−1
current_alpha	0.0000
highest_alpha	2715000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.993

Unit Cell

length_a	31.136 Å
length_b	57.158 Å
length_c	96.910 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

Symmetry

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

Refinement

resolution	1.470 Å
resolution_low	29.640 Å
r_factor	0.1876
r_work	0.1862
r_free	0.2127

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/y0/9y0q/pr_distribution.json
• pr_output /app/data/pr_computation/y0/9y0q/9y0q.pr.out
• pr_plot /app/data/visualization/pr_computation/y0/9y0q/9y0q_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/y0/9y0q/9y0q.dat
• saxs_fit /app/data/saxs_computation/y0/9y0q/9y0q.fit
• saxs_log /app/data/saxs_computation/y0/9y0q/9y0q.log
• saxs_plot /app/data/visualization/saxs_computation/y0/9y0q/9y0q_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/y0/9y0q/9y0q.fit
pddf	/app/data/pr_computation/y0/9y0q/9y0q.pr.out
profile	/app/data/saxs_computation/y0/9y0q/9y0q.dat