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9pre

Crystal structure of oxidised E.coli DsbA in complex with propiolic acid

Method: X-RAY DIFFRACTION D_max: 59.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pre
deposition_date	2025-07-24
title	Crystal structure of oxidised E.coli DsbA in complex with propiolic acid
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	17.86 Å
rg_electron	16.65 Å
i0	8181760.00
molecular_weight	21132.0 kDa
excluded_volume	26336 Å³
envelope_volume	29627 Å³
shell_volume	15191 Å³
envelope_diameter	59.2 Å
shell_rg	22.25 Å
envelope_rg	16.92 Å
shape_rg	16.64 Å
total_rg	17.62 Å
total_atoms	2878
n_residues	188
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	59.2 Å
rg_real	18.30 Å
rg_real_error	0.11 Å
i0_real	8.1020e+06
i0_real_error	8.8490e+04
rg_reciprocal	17.82 Å
i0_reciprocal	8182000.0000
total_estimate	0.6627
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	56.0 Å
skewness	0.408
kurtosis	-0.141
angular_range	— – 0.4450 Å⁻¹
current_alpha	7.5170
highest_alpha	2665000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 0.920; Sysdev: 0.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.305

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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	21025.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3215

AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK

Source

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

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	3-{3-[(5-methyl-1,2-oxazole-3-carbonyl)amino]phenyl}prop-2-ynoic acid
formula_weight	270.2 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	253

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6. Citations (1)

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length_a	100.561 Å
length_b	100.561 Å
length_c	45.908 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.680 Å
resolution_low	44.970 Å
r_factor	0.1575
r_work	0.1562
r_free	0.1823

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

Crystal structure of oxidised E.coli DsbA in complex with propiolic acid

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