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9v52

Structure of TolC and YbjP closed state complex

Method: ELECTRON MICROSCOPY D_max: 144.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v52
deposition_date	2025-05-25
title	Structure of TolC and YbjP closed state complex
keywords	Multidrug efflux pump, TolC, YbjP, AcrA, AcrB, lipoprotein, antibiotic resistance, Gram-negative, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	41.77 Å
rg_electron	41.21 Å
i0	613951000.00
molecular_weight	192350.0 kDa
excluded_volume	237110 Å³
envelope_volume	353060 Å³
shell_volume	72511 Å³
envelope_diameter	153.0 Å
shell_rg	46.33 Å
envelope_rg	40.29 Å
shape_rg	41.21 Å
total_rg	41.48 Å
total_atoms	13539
n_residues	1752
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	144.0 Å
rg_real	41.74 Å
rg_real_error	1.35 Å
i0_real	6.1400e+08
i0_real_error	1.1690e+07
rg_reciprocal	41.77 Å
i0_reciprocal	614000000.0000
total_estimate	0.8411
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	53.0 Å
skewness	0.407
kurtosis	0.157
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	58720000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.723; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.769

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Outer membrane protein TolC
formula_weight	53783.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C1,C3,C2
atom_count	13539

MKKLLPILIGLSLSGFSSLSQAENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN

Source

organism	Escherichia coli (strain K12)
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 2 polymer

description	Uncharacterized lipoprotein YbjP
formula_weight	19013.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	P1,P3,P2

MRYSKLTMLIPCALLLSACTTVTPAYKDNGTRSGPCVEGGPDNVAQQFYDYRILHRSNDITALRPYLSDKLATLLSDASRDNNHRELLTNDPFSSRTTLPDSAHVASASTIPNRDARNIPLRVDLKQGDQGWQDEVLMIQEGQCWVIDDVRYLGGSVHATAGTLRQSIENR

Source

organism	Escherichia coli (strain K12)
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

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6. Citations (2)

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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	triclinic

resolution	3.56 Å
resolution_method	—
num_particles	63022

fit	/app/data/saxs_computation/v5/9v52/9v52.fit
pddf	/app/data/pr_computation/v5/9v52/9v52.pr.out
profile	/app/data/saxs_computation/v5/9v52/9v52.dat

Structure of TolC and YbjP closed state complex

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)