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9vnd

Structure of the Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 Heterohexamer in Complex with the Effector Bte1

Method: ELECTRON MICROSCOPY D_max: 82.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vnd
deposition_date	2025-06-30
title	Structure of the Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 Heterohexamer in Complex with the Effector Bte1
keywords	Bacteroides fragilis, T6SS, Hcp, effector, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	26.71 Å
rg_electron	26.06 Å
i0	41530700.00
molecular_weight	52236.0 kDa
excluded_volume	66527 Å³
envelope_volume	92784 Å³
shell_volume	30074 Å³
envelope_diameter	85.6 Å
shell_rg	33.12 Å
envelope_rg	25.47 Å
shape_rg	26.01 Å
total_rg	27.10 Å
total_atoms	3685
n_residues	457
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	82.0 Å
rg_real	26.60 Å
rg_real_error	0.46 Å
i0_real	4.1530e+07
i0_real_error	5.8850e+05
rg_reciprocal	26.64 Å
i0_reciprocal	41530000.0000
total_estimate	0.9141
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.8 Å
skewness	0.154
kurtosis	-0.573
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	5405000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.969

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Bacteroides fragilis NCTC9343 T6SS Hcp3
formula_weight	15389.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E
atom_count	3685

MELFSFLQVDSDLTAWFILDGQEYEMSHFDINFAQSVDHKGQPQDEVRGGIMSITLSQTLPENIYRWGMTSIPKNGSVIFKSKTTNPPLKINFINAYCIRFNRSIANEGGLESQLVISPDEMLINGISFDNHWVK

Source

organism	Bacteroides fragilis NCTC 9343
ncbi_taxonomy_id	272559
host_organism	Escherichia coli

Entity 2 polymer

description	Bacteroides fragilis NCTC9343 T6SS Hcp2
formula_weight	16112.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,A,D,F

MFGHKSFLRIGALGDSSISGLYKDSYELENCHFSFNQGTNTDGKPQTDVRGGTLYLTYAGLPQDDMLRWILNSKKYEDGAIVICDDSDEPLEKILFEQAACTGLNIEYTQKGKAYIHTKIILQVRKIKVGETTFENRWTINE

Source

organism	Bacteroides fragilis NCTC 9343
ncbi_taxonomy_id	272559
host_organism	Escherichia coli

Entity 3 polymer

description	Bacteroides fragilis NCTC9343 T6SS V1 effector Bte1
formula_weight	32879.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MGKEIEIKKLPEFEAMVNAGNTTYTGLVEGIGYVYWTTETLYFIRTNPEQLWAIPKYQQIPFPYFQRKDAIIETKTLHTLHVLSKDELLKLDYDAYYAFYGIVEEMLKFIHRADAIKSYCEIPLPIIKSKGALKGNDARNGILSLGSQINDQIGAPLDAANMLMDNKHIGKIGDGLSLISIIDEVGNGEYWSAAGDILLFAAGKTKLSPYMTVISLGTWMYETDLMQWRLACINYSDYKKTLIKYRELQKKFESGDKSVEEKMNECHKILNSHYIEMQKNLGNLGVKF

Source

organism	Bacteroides fragilis NCTC 9343
ncbi_taxonomy_id	272559
host_organism	Escherichia coli

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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	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	60133

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

Structure of the Bacteroides fragilis NCTC9343 T6SS Hcp2-Hcp3 Heterohexamer in Complex with the Effector Bte1

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 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)