Cryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus

Method: ELECTRON MICROSCOPY D_max: 179.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wfd
deposition_date	2025-08-21
last_revision	2025-11-19
title	Cryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus
keywords	--Type II secretion system protein, Acidithiobacillus caldus, 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	66.59 Å
rg_electron	66.17 Å
i0	5579570000.00
molecular_weight	643520.0 kDa
excluded_volume	811780 Å³
envelope_volume	1510900 Å³
shell_volume	185510 Å³
envelope_diameter	189.6 Å
shell_rg	75.61 Å
envelope_rg	61.75 Å
shape_rg	66.18 Å
total_rg	66.30 Å
total_atoms	45332
n_residues	6034
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	179.6 Å
rg_real	65.89 Å
rg_real_error	0.75 Å
i0_real	5.5800e+09
i0_real_error	9.9810e+07
rg_reciprocal	67.17 Å
i0_reciprocal	5592000000.0000
total_estimate	0.8310
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	97.3 Å
skewness	-0.044
kurtosis	-0.426
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0000
highest_alpha	614600000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.013

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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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	2.390 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.39 Å
resolution_method	—
num_particles	72834

description	Type II and III secretion system protein
formula_weight	53556.2 kDa
src_method	man
entity_count	14

Cryo-EM structure of the Type II secretion system protein from Acidithiobacillus caldus

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
atom_count	45332

organism	Acidithiobacillus caldus (strain SM-1)
ncbi_taxonomy_id	990288
host_organism	Escherichia coli

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