Heptameric pore structure of Vibrio cholerae Cytolysin (VCC) embedded in lipid bilayer

Method: ELECTRON MICROSCOPY D_max: 153.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ue9
deposition_date	2025-04-08
title	Heptameric pore structure of Vibrio cholerae Cytolysin (VCC) embedded in lipid bilayer
keywords	Vibrio cholerae Cytolysin (VCC), Pore-forming toxin, TOXIN; TOXIN
method	ELECTRON MICROSCOPY

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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	51.40 Å
rg_electron	50.45 Å
i0	3004410000.00
molecular_weight	440440.0 kDa
excluded_volume	542570 Å³
envelope_volume	824500 Å³
shell_volume	128330 Å³
envelope_diameter	153.0 Å
shell_rg	60.56 Å
envelope_rg	48.79 Å
shape_rg	50.45 Å
total_rg	50.74 Å
total_atoms	31131
n_residues	4067
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	153.0 Å
rg_real	51.05 Å
rg_real_error	0.71 Å
i0_real	3.0040e+09
i0_real_error	4.6380e+07
rg_reciprocal	51.68 Å
i0_reciprocal	3007000000.0000
total_estimate	0.8814
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.1 Å
skewness	-0.044
kurtosis	-0.542
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	565100000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.785

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	4.000 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.00 Å
resolution_method	—
num_particles	117427

description	HlyA
formula_weight	64605.1 kDa
src_method	man
entity_count	7

Heptameric pore structure of Vibrio cholerae Cytolysin (VCC) embedded in lipid bilayer

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Vibrio cholerae
ncbi_taxonomy_id	666
host_organism	Escherichia coli

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	362

fit	/app/data/saxs_computation/ue/9ue9/9ue9.fit
pddf	/app/data/pr_computation/ue/9ue9/9ue9.pr.out
profile	/app/data/saxs_computation/ue/9ue9/9ue9.dat

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G
atom_count	31493