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9veg

Structural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis

Method: ELECTRON MICROSCOPY D_max: 166.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9veg
deposition_date	2025-06-09
title	Structural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis
keywords	binary toxin, biopesticide, 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	51.34 Å
rg_electron	51.13 Å
i0	1587440000.00
molecular_weight	327960.0 kDa
excluded_volume	408790 Å³
envelope_volume	604840 Å³
shell_volume	98077 Å³
envelope_diameter	177.1 Å
shell_rg	55.31 Å
envelope_rg	50.09 Å
shape_rg	51.13 Å
total_rg	51.27 Å
total_atoms	23058
n_residues	2947
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	166.4 Å
rg_real	51.26 Å
rg_real_error	1.54 Å
i0_real	1.5870e+09
i0_real_error	3.0180e+07
rg_reciprocal	51.40 Å
i0_reciprocal	1588000000.0000
total_estimate	0.8746
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	59.0 Å
skewness	0.297
kurtosis	-0.269
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	96430000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.757

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Vip1
formula_weight	72654.5 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,F,G
atom_count	23058

DEDTDTDGDSIPDLWEENGYTIQNRIAVKWDDSLASKGYTKFVSNPLDSHTVGDPYTDYEKAARDLDMSNAKETFNPLVAAFPSVNVNMEKVILSPNKNLSNSVESHSSTNWSYTNTVGASVEAGFGPKGLSFGVSASYQHSETVAQEWGTSKGNTSQFNTASAGYLNANVRYNNVGTGAIYEVKPTTSFVLDKNTIATITAKSNSTALNISPGESYPKKGQNGIAITSMDDFNSHPITLNKQQVDQLLNNKPMMLETNQTDGVYKIKDTHGNIVTGGEWNGVTQQIKAKTASIIVDNGERVSEKRVAAKDYDYPEDKTPSLTLKDALKLSYPDEIKETDGLLYYNDKPIYESSVMTYLDENTAKEVKKQLNDTTGKFKDVNHLYDVKLTPRMNFTIKMSSLYDGAEGGSSSKPIGTWYNTSYVNGGNTGKKQFQSANSNAYVALSSEAKKKLNQSVNYYLSMYMKADSTTEPTVEVVGAKSTITSKKVKLNNQGYQRVDILVKNSERNLIDKIYIKGNGKTNVYWDDVTISEISAINPASLSDIEIQEIFKDSTIQYGNPSFAIDFITFKNIKPLQNYIKQYEIYQKIVGIDLGTGKEVITENTFNTEGDLKEDGSVKIDVRKNGFGFITFKGSNLKIQAIANDGRKIEVFNKIF

Source

organism	Bacillus thuringiensis
ncbi_taxonomy_id	1428
host_organism	Bacillus thuringiensis

Entity 2 polymer

description	Vip2
formula_weight	45389.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

KAEDFKEDKEKAKEWGKEKEKEWKLTATEKGKMNDFLNDKNKIKTNYKEITFSMAGSFEDEMKNLKEIDKMFDKANLSSSIITYKNVEPATIGFNKSLIEGNTINSDALAQFKEQFLDRDMKFDSYLDTHLTAQQVSSKERVIMKVTVPSGKGSTTPTKAGVILNNNEYKMLIDNGYVLHVDKVSKVVKKGFECVQVEGILKKSLDFKNDINAESHSWGMKNYEGWAKNLTDSQREALDGYARQDYKEINDYLRNQGGSGNEKLDAQIKNISEALGKKPIPENITVYRWCGMPEFGYQISDPLPSLKDFEEKFLNTIKEDKGYMSTSLSSERLAAFGSRKIILRLQVPKGSTGAYLSAIGGFASEKEILLDKDSKYHIDKVTEVVIKGVKRYVIDATLLT

Source

organism	Bacillus thuringiensis
ncbi_taxonomy_id	1428
host_organism	Bacillus thuringiensis

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	14

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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	3.050 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.05 Å
resolution_method	—
num_particles	107143

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

Structural basis for the assembly and translocation of the Vip1-Vip2 insecticidal binary toxin from Bacillus thuringiensis

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)