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

entry_id	9y0p
deposition_date	2025-08-28
title	Crystal structure of Escherichia coli DsbA C33A mutant in complex with a peptide derived from LptD - Binding mode I
keywords	Thiol oxidase mutant, bacterial foldase, thioredoxin fold, complex, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

rg_guinier	24.75 Å
rg_electron	23.62 Å
i0	33967300.00
molecular_weight	44794.0 kDa
excluded_volume	55920 ų
envelope_volume	68582 ų
shell_volume	24148 ų
envelope_diameter	78.9 Å
shell_rg	30.62 Å
envelope_rg	23.45 Å
shape_rg	23.60 Å
total_rg	24.51 Å
total_atoms	3162
n_residues	397
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	76.8 Å
rg_real	24.67 Å
rg_real_error	0.56 Å
i0_real	3.3970e+07
i0_real_error	5.0400e+05
rg_reciprocal	24.69 Å
i0_reciprocal	33970000.0000
total_estimate	0.9123
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	75.5 Å
skewness	0.210
kurtosis	-0.569
angular_range	— – 0.3200 Å−1
current_alpha	0.0000
highest_alpha	11420000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.993

Unit Cell

length_a	68.210 Å
length_b	79.335 Å
length_c	82.503 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

Symmetry

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

Refinement

resolution	1.470 Å
resolution_low	43.820 Å
r_factor	0.1897
r_work	0.1886
r_free	0.2097

Diffraction

temperature

100.0 K

Files (7)

• pr_distribution /app/data/pr_computation/y0/9y0p/pr_distribution.json
• pr_output /app/data/pr_computation/y0/9y0p/9y0p.pr.out
• pr_plot /app/data/visualization/pr_computation/y0/9y0p/9y0p_pr_distribution.png
• saxs_curve_dat /app/data/saxs_computation/y0/9y0p/9y0p.dat
• saxs_fit /app/data/saxs_computation/y0/9y0p/9y0p.fit
• saxs_log /app/data/saxs_computation/y0/9y0p/9y0p.log
• saxs_plot /app/data/visualization/saxs_computation/y0/9y0p/9y0p_saxs_profile.png

Curves (3)

fit	/app/data/saxs_computation/y0/9y0p/9y0p.fit
pddf	/app/data/pr_computation/y0/9y0p/9y0p.pr.out
profile	/app/data/saxs_computation/y0/9y0p/9y0p.dat