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9y0m

Crystal structure of Escherichia coli DsbA P151T mutant

Method: X-RAY DIFFRACTION D_max: 103.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y0m
deposition_date	2025-08-28
title	Crystal structure of Escherichia coli DsbA P151T mutant
keywords	Thiol oxidase mutant, bacterial foldase, thioredoxin fold, OXIDOREDUCTASE; OXIDOREDUCTASE
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	32.51 Å
rg_electron	31.97 Å
i0	109505000.00
molecular_weight	84469.0 kDa
excluded_volume	106160 Å³
envelope_volume	137220 Å³
shell_volume	35978 Å³
envelope_diameter	110.8 Å
shell_rg	38.64 Å
envelope_rg	31.86 Å
shape_rg	31.97 Å
total_rg	32.56 Å
total_atoms	5998
n_residues	751
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	103.3 Å
rg_real	32.50 Å
rg_real_error	0.78 Å
i0_real	1.0950e+08
i0_real_error	1.6440e+06
rg_reciprocal	32.51 Å
i0_reciprocal	109500000.0000
total_estimate	0.9013
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.1 Å
skewness	0.270
kurtosis	-0.573
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	18840000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.884

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Thiol:disulfide interchange protein DsbA
formula_weight	21246.1 kDa
ec_number	1.8.4.15
mutation	P151T
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	6008

SAQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVTAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEKK

Source

organism	Escherichia coli
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	10

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6. Citations (1)

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length_a	63.762 Å
length_b	79.750 Å
length_c	103.893 Å
angle_alpha	90.00 °
angle_beta	90.19 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.880 Å
resolution_low	44.950 Å
r_factor	0.2118
r_work	0.2090
r_free	0.2682

fit	/app/data/saxs_computation/y0/9y0m/9y0m.fit
pddf	/app/data/pr_computation/y0/9y0m/9y0m.pr.out
profile	/app/data/saxs_computation/y0/9y0m/9y0m.dat

Crystal structure of Escherichia coli DsbA P151T mutant

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