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9prk

Crystal structure of E.coli DsbA in complex with analogue 17

Method: X-RAY DIFFRACTION D_max: 70.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9prk
deposition_date	2025-07-24
title	Crystal structure of E.coli DsbA in complex with analogue 17
keywords	Oxidoreductase, Oxidoreductase inhibitor, DsbA, bacteria, enzyme; 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	22.65 Å
rg_electron	21.82 Å
i0	52434400.00
molecular_weight	38375.0 kDa
excluded_volume	37516 Å³
envelope_volume	61123 Å³
shell_volume	23504 Å³
envelope_diameter	72.8 Å
shell_rg	28.39 Å
envelope_rg	21.70 Å
shape_rg	21.80 Å
total_rg	22.46 Å
total_atoms	2929
n_residues	373
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	70.8 Å
rg_real	22.56 Å
rg_real_error	0.35 Å
i0_real	5.2430e+07
i0_real_error	5.9000e+05
rg_reciprocal	22.58 Å
i0_reciprocal	52440000.0000
total_estimate	0.7341
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	27.9 Å
skewness	0.185
kurtosis	-0.535
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	15130000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 1.000; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Thiol:disulfide interchange protein DsbA
formula_weight	21025.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3118

AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	methyl {2,6-difluoro-4-[(2S)-3-hydroxy-2-(3-{3-[(5-methyl-1,2-oxazole-3-carbonyl)amino]phenyl}prop-2-ynamido)propyl]phenyl}acetate
formula_weight	511.5 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	161

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6. Citations (1)

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length_a	36.081 Å
length_b	87.095 Å
length_c	50.188 Å
angle_alpha	90.00 °
angle_beta	101.19 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.760 Å
resolution_low	43.550 Å
r_factor	0.1903
r_work	0.1880
r_free	0.2348

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

Crystal structure of E.coli DsbA in complex with analogue 17

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