SAXSdb — 9qgy

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1. Structure Basics

entry_id	9qgy
deposition_date	2025-03-14
title	Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite efflux pump
keywords	multi-drug efflux pump, MacAB-TolC, AcrABZ-TolC, type I secretion, lipoprotein, membrane protein assembly, 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	83.56 Å
rg_electron	85.04 Å
i0	3097850000.00
molecular_weight	461900.0 kDa
excluded_volume	575720 Å³
envelope_volume	945870 Å³
shell_volume	103740 Å³
envelope_diameter	291.9 Å
shell_rg	63.00 Å
envelope_rg	83.44 Å
shape_rg	85.09 Å
total_rg	84.53 Å
total_atoms	64967
n_residues	4198
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	227.8 Å
rg_real	78.91 Å
rg_real_error	1.02 Å
i0_real	2.9730e+09
i0_real_error	5.5690e+07
rg_reciprocal	78.58 Å
i0_reciprocal	3054000000.0000
total_estimate	0.8252
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	60.0 Å
skewness	0.432
kurtosis	-0.920
angular_range	— – 0.0950 Å⁻¹
current_alpha	0.8833
highest_alpha	523100000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.669; Stabil: 0.960; Sysdev: 1.000; Positv: 1.000; Valcen: 0.840; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Outer membrane protein TolC
formula_weight	51495.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	64989

ENLMQVYQQARLSNPELRKSAADRDAAFEKINEARSPLLPQLGLGADYTYSNGYRDANGINSNATSASLQLTQSIFDMSKWRALTLQEKAAGIQDVTYQTDQQTLILNTATAYFNVLNAIDVLSYTQAQKEAIYRQLDQTTQRFNVGLVAITDVQNARAQYDTVLANEVTARNNLDNAVEQLRQITGNYYPELAALNVENFKTDKPQPVNALLKEAEKRNLSLLQARLSQDLAREQIRQAQDGHLPTLDLTASTGISDTSYSGSKTRGAAGTQYDDSNMGQNKVGLSFSLPIYQGGMVNSQVKQAQYNFVGASEQLESAHRSVVQTVRSSFNNINASISSINAYKQAVVSAQSSLDAMEAGYSVGTRTIVDVLDATTTLYNAKQELANARYNYLINQLNIKSALGTLNEQDLLALNNALSKPVSTNPENVAPQTPEQNAIADGYAPDSPAPVVQQTSARTTTSNGHNPFRN

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	Uncharacterized lipoprotein YbjP
formula_weight	17004.7 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

CTTVTPAYKDNGTRSGPCVEGGPDNVAQQFYDYRILHRSNDITALRPYLSDKLATLLSDASRDNNHRELLTNDPFSSRTTLPDSAHVASASTIPNRDARNIPLRVDLKQGDQGWQDEVLMIQEGQCWVIDDVRYLGGSVHATAGTLRQSIENR

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 polymer

description	Macrolide export protein MacA
formula_weight	40672.8 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	G,H,I,J,K,L

MKKRKTVKKRYVIALVIVIAGLITLWRILNAPVPTYQTLIVRPGDLQQSVLATGKLDALRKVDVGAQVSGQLKTLSVAIGDKVKKDQLLGVIDPEQAENQIKEVEATLMELRAQRQQAEAELKLARVTYSRQQRLAQTKAVSQQDLDTAATEMAVKQAQIGTIDAQIKRNQASLDTAKTNLDYTRIVAPMAGEVTQITTLQGQTVIAAQQAPNILTLADMSAMLVKAQVSEADVIHLKPGQKAWFTVLGDPLTRYEGQIKDVLPTPEKVNDAIFYYARFEVPNPNGLLRLDMTAQVHIQLTDVKNVLTIPLSALGDPVGDNRYKVKLLRNGETREREVTIGARNDTDVEIVKGLEAGDEVVIGEAKPGAAQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 4 polymer

description	Macrolide export ATP-binding/permease protein MacB
formula_weight	23354.3 kDa
ec_number	7.6.2.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,N

MVLADIRSIGTNTIDVYPGKDFGDDDPQYQQALKYDDLIAIQKQPWVASATPAVSQNLRLRYNNVDVAASANGVSGDYFNVYGMTFSEGNTFNQEQLNGRAQVVVLDSNTRRQLFPHKADVVGEVILVGNMPARVIGVAEEKQSMFGSSKVLRVWLPYSTMSGRVMGQSWLNSITVRVKEGFDSAEAEQQLTRLLSLRHGKKDFFTWNM

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	(2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
formula_weight	568.9 kDa
src_method	syn
entity_count	3

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	22

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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	2.480 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.48 Å
resolution_method	—
num_particles	233775

fit	/app/data/saxs_computation/qg/9qgy/9qgy.fit
pddf	/app/data/pr_computation/qg/9qgy/9qgy.pr.out
profile	/app/data/saxs_computation/qg/9qgy/9qgy.dat

Structure of the YbjP lipoprotein bound to the MacAB-TolC tripartite 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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)