SAXSdb — 9tg4

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1. Structure Basics

entry_id	9tg4
deposition_date	2025-11-28
title	Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump
keywords	;Multi-drug efflux pump, RND transporter, MacAB-TolC, AcrABZ-TolC, type I secretion, lipoprotein, membrane protein assembly, MEMBRANE PROTEIN, TRANSPORT PROTEIN ;; TRANSPORT 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	92.42 Å
rg_electron	94.81 Å
i0	7936950000.00
molecular_weight	762560.0 kDa
excluded_volume	958850 Å³
envelope_volume	1510800 Å³
shell_volume	154930 Å³
envelope_diameter	346.4 Å
shell_rg	65.28 Å
envelope_rg	95.84 Å
shape_rg	94.82 Å
total_rg	94.38 Å
total_atoms	53653
n_residues	7048
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	260.8 Å
rg_real	86.46 Å
rg_real_error	1.45 Å
i0_real	7.6110e+09
i0_real_error	1.5500e+08
rg_reciprocal	83.66 Å
i0_reciprocal	7729000000.0000
total_estimate	0.8298
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	61.4 Å
skewness	0.564
kurtosis	-0.659
angular_range	— – 0.0850 Å⁻¹
current_alpha	0.4936
highest_alpha	1357000000.0000
n_real_points	18
gnom_version	4.1.3
quality_criteria	AN1: 0.002; Oscil: 0.615; Stabil: 0.979; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.032

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Outer membrane protein TolC
formula_weight	52623.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	53653

MENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRNDYKDDDDK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	D,E,F,G,H,I

MNKNRGFTPLAVVLMLSGSLALTGCDDKQAQQGGQQMPAVGVVTVKTEPLQITTELPGRTSAYRIAEVRPQVSGIILKRNFKEGSDIEAGVSLYQIDPATYQATYDSAKGDLAKAQAAANIAQLTVNRYQKLLGTQYISKQEYDQALADAQQANAAVTAAKAAVETARINLAYTKVTSPISGRIGKSNVTEGALVQNGQATALATVQQLDPIYVDVTQSSNDFLRLKQELANGTLKQENGKAKVSLITSDGIKFPQDGTLEFSDVTVDQTTGSITLRAIFPNPDHTLLPGMFVRARLEEGLNPNAILVPQQGVTRTPRGDATVLVVGADDKVETRPIVASQAIGDKWLVTEGLKAGDRVVISGLQKVRPGVQVKAQEVTADNNQQAASGAQPEQSKS

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 polymer

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

Polymer

type	polypeptide(L)
strand_id	J,K,L

MPNFFIDRPIFAWVIAIIIMLAGGLAILKLPVAQYPTIAPPAVTISASYPGADAKTVQDTVTQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESGTDADIAQVQVQNKLQLAMPLLPQEVQQQGVSVEKSSSSFLMVVGVINTDGTMTQEDISDYVAANMKDAISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVITAIKAQNAQVAAGQLGGTPPVKGQQLNASIIAQTRLTSTEEFGKILLKVNQDGSRVLLRDVAKIELGGENYDIIAEFNGQPASGLGIKLATGANALDTAAAIRAELAKMEPFFPSGLKIVYPYDTTPFVKISIHEVVKTLVEAIILVFLVMYLFLQNFRATLIPTIAVPVVLLGTFAVLAAFGFSINTLTMFGMVLAIGLLVDDAIVVVENVERVMAEEGLPPKEATRKSMGQIQGALVGIAMVLSAVFVPMAFFGGSTGAIYRQFSITIVSAMALSVLVALILTPALCATMLKPIAKGDHGEGKKGFFGWFNRMFEKSTHHYTDSVGGILRSTGRYLVLYLIIVVGMAYLFVRLPSSFLPDEDQGVFMTMVQLPAGATQERTQKVLNEVTHYYLTKEKNNVESVFAVNGFGFAGRGQNTGIAFVSLKDWADRPGEENKVEAITMRATRAFSQIKDAMVFAFNLPAIVELGTATGFDFELIDQAGLGHEKLTQARNQLLAEAAKHPDMLTSVRPNGLEDTPQFKIDIDQEKAQALGVSINDINTTLGAAWGGSYVNDFIDRGRVKKVYVMSEAKYRMLPDDIGDWYVRAADGQMVPFSAFSSSRWEYGSPRLERYNGLPSMEILGQAAPGKSTGEAMELMEQLASKLPTGVGYDWTGMSYQERLSGNQAPSLYAISLIVVFLCLAALYESWSIPFSVMLVVPLGVIGALLAATFRGLTNDVYFQVGLLTTIGLSAKNAILIVEFAKDLMDKEGKGLIEATLDAVRMRLRPILMTSLAFILGVMPLVISTGAGSGAQNAVGTGVMGGMVTATVLAIFFVPVFFVVVRRRFSRKNEDIEHSHTVDHH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 4 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	M,N,O

MLELLKSLVFAVIMVPVVMAIILGLIYGLGEVFNIFSGVGKKDQPGQNH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 5 polymer

description	Uncharacterized lipoprotein YbjP
formula_weight	18122.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	P,Q,R

MDNGTRSGPCVEGGPDNVAQQFYDYRILHRSNDITALRPYLSDKLATLLSDASRDNNHRELLTNDPFSSRTTLPDSAHVASASTIPNRDARNIPLRVDLKQGDQGWQDEVLMIQEGQCWVIDDVRYLGGSVHATAGTLRQSIENRENLYFQSLEHHHHHH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

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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	3.170 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.17 Å
resolution_method	—
num_particles	97441

fit	/app/data/saxs_computation/tg/9tg4/9tg4.fit
pddf	/app/data/pr_computation/tg/9tg4/9tg4.pr.out
profile	/app/data/saxs_computation/tg/9tg4/9tg4.dat

Structure of the YbjP lipoprotein bound to the AcrABZ-TolC efflux pump

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 (6)

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

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)