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9prf

Crystal structure of E.coli DsbA in-complex with analogue 6

Method: X-RAY DIFFRACTION D_max: 87.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9prf
deposition_date	2025-07-24
title	Crystal structure of E.coli DsbA in-complex with analogue 6
keywords	Oxidoreductase, Oxidoreductase inhibitor; 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	25.50 Å
rg_electron	25.04 Å
i0	53032100.00
molecular_weight	38556.0 kDa
excluded_volume	37594 Å³
envelope_volume	62400 Å³
shell_volume	22064 Å³
envelope_diameter	90.1 Å
shell_rg	30.44 Å
envelope_rg	25.08 Å
shape_rg	25.03 Å
total_rg	25.54 Å
total_atoms	2920
n_residues	372
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	87.9 Å
rg_real	25.66 Å
rg_real_error	0.68 Å
i0_real	5.3030e+07
i0_real_error	7.5730e+05
rg_reciprocal	25.61 Å
i0_reciprocal	53030000.0000
total_estimate	0.8516
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	86.5 Å
skewness	0.494
kurtosis	-0.289
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	15570000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.807; Smooth: 0.907

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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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3285

AQYEDGKQYTTLEKPVAGAPQVLEFFSFFCPHCYQFEEVLHISDNVKKKLPEGVKMTKYHVNFMGGDLGKDLTQAWAVAMALGVEDKVTVPLFEGVQKTQTIRSASDIRDVFINAGIKGEEYDAAWNSFVVKSLVAQQEKAAADVQLRGVPAMFVNGKYQLNPQGMDTSNMDVFVQQYADTVKYLSEK

Source

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

Entity 2 non-polymer

description	N-[3-(3-{[(2S)-2-hydroxybutyl]amino}-3-oxoprop-1-yn-1-yl)phenyl]-5-methyl-1,2-oxazole-3-carboxamide
formula_weight	341.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	N-[3-(3-{[(2R)-2-hydroxybutyl]amino}-3-oxoprop-1-yn-1-yl)phenyl]-5-methyl-1,2-oxazole-3-carboxamide
formula_weight	341.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	352

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6. Citations (1)

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length_a	41.625 Å
length_b	55.211 Å
length_c	75.952 Å
angle_alpha	90.00 °
angle_beta	100.40 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.610 Å
resolution_low	44.400 Å
r_factor	0.1938
r_work	0.1928
r_free	0.2150

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

Crystal structure of E.coli DsbA in-complex with analogue 6

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