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9prl

Crystal structure of E.coli DsbA in complex with analogue 18

Method: X-RAY DIFFRACTION D_max: 75.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9prl
deposition_date	2025-07-24
title	Crystal structure of E.coli DsbA in complex with analogue 18
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	23.19 Å
rg_electron	22.38 Å
i0	54774300.00
molecular_weight	39476.0 kDa
excluded_volume	38721 Å³
envelope_volume	60870 Å³
shell_volume	22990 Å³
envelope_diameter	78.8 Å
shell_rg	28.87 Å
envelope_rg	22.53 Å
shape_rg	22.31 Å
total_rg	23.10 Å
total_atoms	3033
n_residues	374
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	75.9 Å
rg_real	23.15 Å
rg_real_error	0.46 Å
i0_real	5.4770e+07
i0_real_error	6.9980e+05
rg_reciprocal	23.16 Å
i0_reciprocal	54770000.0000
total_estimate	0.8982
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	74.8 Å
skewness	0.277
kurtosis	-0.444
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	15450000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.994

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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	20954.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3315

QYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK

Source

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

Entity 2 non-polymer

description	methyl {2-chloro-4-[(2S)-3-hydroxy-2-(3-{3-[(5-methyl-1,2-oxazole-3-carbonyl)amino]phenyl}prop-2-ynamido)propyl]phenyl}acetate
formula_weight	509.9 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	263

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6. Citations (1)

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length_a	48.905 Å
length_b	97.552 Å
length_c	100.940 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.910 Å
resolution_low	44.010 Å
r_factor	0.1882
r_work	0.1863
r_free	0.2249

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

Crystal structure of E.coli DsbA in complex with analogue 18

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