SAXSdb — 9v53

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1. Structure Basics

entry_id	9v53
deposition_date	2025-05-25
title	Structure of TolC, YbjP, and AcrABZ 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	94.12 Å
rg_electron	96.74 Å
i0	7874680000.00
molecular_weight	759810.0 kDa
excluded_volume	955540 Å³
envelope_volume	1566200 Å³
shell_volume	158670 Å³
envelope_diameter	356.3 Å
shell_rg	66.02 Å
envelope_rg	97.02 Å
shape_rg	96.75 Å
total_rg	96.27 Å
total_atoms	53464
n_residues	7037
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	268.4 Å
rg_real	88.43 Å
rg_real_error	1.61 Å
i0_real	7.5570e+09
i0_real_error	1.4970e+08
rg_reciprocal	84.73 Å
i0_reciprocal	7650000000.0000
total_estimate	0.8222
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	67.1 Å
skewness	0.569
kurtosis	-0.651
angular_range	— – 0.0800 Å⁻¹
current_alpha	0.6433
highest_alpha	1235000000.0000
n_real_points	17
gnom_version	4.1.3
quality_criteria	AN1: 0.009; Oscil: 0.604; Stabil: 0.955; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.029

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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,C2,C3
atom_count	53464

MKKLLPILIGLSLSGFSSLSQAENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN

Source

organism	Escherichia coli K-12
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,P2,P3

MRYSKLTMLIPCALLLSACTTVTPAYKDNGTRSGPCVEGGPDNVAQQFYDYRILHRSNDITALRPYLSDKLATLLSDASRDNNHRELLTNDPFSSRTTLPDSAHVASASTIPNRDARNIPLRVDLKQGDQGWQDEVLMIQEGQCWVIDDVRYLGGSVHATAGTLRQSIENR

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 3 polymer

description	Multidrug efflux pump subunit AcrA
formula_weight	42237.5 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A1,A2,A3,a2,a1,a3

MNKNRGFTPLAVVLMLSGSLALTGCDDKQAQQGGQQMPAVGVVTVKTEPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFKEGSDIEAGVSLYQIDPATYQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQEYDQALADAQQANAAVTAAKAAVETARINLAYTKVTSPISGRIGKSNVTEGALVQNGQATALATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVSLITSDGIKFPQDGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGLNPNAILVPQQGVTRTPRGDATVLVVGADDKVETRPIVASQAIGDKWLVTEGLKAGDRVVISGLQKVRPGVQVKAQEVTADNNQQAASGAQPEQSKS

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 4 polymer

description	Multidrug efflux pump subunit AcrB
formula_weight	113665.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	BL,BT,BO

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHH

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli

Entity 5 polymer

description	Multidrug efflux pump accessory protein AcrZ
formula_weight	5304.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	ZL,ZT,ZO

MLELLKSLVFAVIMVPVVMAIILGLIYGLGEVFNIFSGVGKKDQPGQNH

Source

organism	Escherichia coli K-12
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	3.39 Å
resolution_method	—
num_particles	31000

fit	/app/data/saxs_computation/v5/9v53/9v53.fit
pddf	/app/data/pr_computation/v5/9v53/9v53.pr.out
profile	/app/data/saxs_computation/v5/9v53/9v53.dat

Structure of TolC, YbjP, and AcrABZ 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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)