SAXSdb — 9qvd

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1. Structure Basics

entry_id	9qvd
deposition_date	2025-04-11
title	cryo-EM structure of TolQRA in nanodiscs
keywords	Molecular motor Multi-pass membrane protein Accumulates at cell constriction sites., MEMBRANE PROTEIN; MEMBRANE 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	36.21 Å
rg_electron	35.46 Å
i0	253458000.00
molecular_weight	135580.0 kDa
excluded_volume	173240 Å³
envelope_volume	249690 Å³
shell_volume	57740 Å³
envelope_diameter	118.8 Å
shell_rg	42.95 Å
envelope_rg	34.59 Å
shape_rg	35.46 Å
total_rg	36.05 Å
total_atoms	9570
n_residues	1220
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	114.0 Å
rg_real	36.04 Å
rg_real_error	0.69 Å
i0_real	2.5350e+08
i0_real_error	3.7450e+06
rg_reciprocal	36.15 Å
i0_reciprocal	253500000.0000
total_estimate	0.8978
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.0 Å
skewness	0.190
kurtosis	-0.459
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	39900000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.962

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Tol-Pal system protein TolQ
formula_weight	25623.7 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	9570

MTDMNILDLFLKASLLVKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRLYQESQGKRDNLTGSEQIFYSGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGSISPYIGLFGTVWGIMHAFIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELNYDNFMEEFTAILHRQAFTVSESNKG

Source

organism	Escherichia coli str. K-12 substr. MG1655
ncbi_taxonomy_id	511145
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Tol-Pal system protein TolR
formula_weight	15398.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,G

MARARGRGRRDLKSEINIVPLLDVLLVLLLIFMATAPIITQSVEVDLPDATESQAVSSNDNPPVIVEVSGIGQYTVVVEKDRLERLPPEQVVAEVSSRFKANPKTVFLIGGAKDVPYDEIIKALNLLHSAGVKSVGLMTQPI

Source

organism	Escherichia coli str. K-12 substr. MG1655
ncbi_taxonomy_id	511145
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Tol-Pal system protein TolA
formula_weight	43232.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	H,I,J

MSKATEQNDKLKRAIIISAVLHVILFAALIWSSFDENIEASAGGGGGSSIDAVMVDSGAVVEQYKRMQSQESSAKRSDEQRKMKEQQAAEELREKQAAEQERLKQLEKERLAAQEQKKQAEEAAKQAELKQKQAEEAAAKAAADAKAKAEADAKAAEEAAKKAAADAKKKAEAEAAKAAAEAQKKAEAAAAALKKKAEAAEAAAAEARKKAATEAAEKAKAEAEKKAAAEKAAADKKAAAEKAAADKKAAEKAAAEKAAADKKAAAEKAAADKKAAAAKAAAEKAAAAKAAAEADDIFGELSSGKNAPKTGGGAKGNNASPAGSGNTKNNGASGADINNYAGQIKSAIESKFYDASSYAGKTCTLRIKLAPDGMLLDIKPEGGDPALCQAALAAAKLAKIPKPPSQAVYEVFKNAPLDFKP

Source

organism	Escherichia coli str. K-12 substr. MG1655
ncbi_taxonomy_id	511145
host_organism	Escherichia coli BL21(DE3)

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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	3.520 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.52 Å
resolution_method	—
num_particles	181301

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

cryo-EM structure of TolQRA in nanodiscs

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)