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9qpr

Single particle cryo-EM structure of the multidrug efflux pump MdtF from Escherichia coli

Method: ELECTRON MICROSCOPY D_max: 144.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpr
deposition_date	2025-03-28
title	Single particle cryo-EM structure of the multidrug efflux pump MdtF from Escherichia coli
keywords	multidrug, pump, anaerobic, lipid, 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	45.35 Å
rg_electron	44.60 Å
i0	1485910000.00
molecular_weight	340590.0 kDa
excluded_volume	434860 Å³
envelope_volume	565690 Å³
shell_volume	99540 Å³
envelope_diameter	144.8 Å
shell_rg	53.85 Å
envelope_rg	44.00 Å
shape_rg	44.62 Å
total_rg	44.89 Å
total_atoms	23905
n_residues	3051
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	144.1 Å
rg_real	45.09 Å
rg_real_error	0.97 Å
i0_real	1.4860e+09
i0_real_error	2.5040e+07
rg_reciprocal	45.35 Å
i0_reciprocal	1486000000.0000
total_estimate	0.8852
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	57.7 Å
skewness	0.155
kurtosis	-0.437
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	305400000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.892

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Multidrug resistance protein MdtF
formula_weight	113759.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,A,B
atom_count	23905

MANYFIDRPVFAWVLAIIMMLAGGLAIMNLPVAQYPQIAPPTITVSATYPGADAQTVEDSVTQVIEQNMNGLDGLMYMSSTSDAAGNASITLTFETGTSPDIAQVQVQNKLQLAMPSLPEAVQQQGISVDKSSSNILMVAAFISDNGSLNQYDIADYVASNIKDPLSRTAGVGSVQLFGSEYAMRIWLDPQKLNKYNLVPSDVISQIKVQNNQISGGQLGGMPQAADQQLNASIIVQTRLQTPEEFGKILLKVQQDGSQVLLRDVARVELGAEDYSTVARYNGKPAAGIAIKLAAGANALDTSRAVKEELNRLSAYFPASLKTVYPYDTTPFIEISIQEVFKTLVEAIILVFLVMYLFLQNFRATIIPTIAVPVVILGTFAILSAVGFTINTLTMFGMVLAIGLLVDDAIVVVENVERVIAEDKLPPKEATHKSMGQIQRALVGIAVVLSAVFMPMAFMSGATGEIYRQFSITLISSMLLSVFVAMSLTPALCATILKAAPEGGHKPNALFARFNTLFEKSTQHYTDSTRSLLRCTGRYMVVYLLICAGMAVLFLRTPTSFLPEEDQGVFMTTAQLPSGATMVNTTKVLQQVTDYYLTKEKDNVQSVFTVGGFGFSGQGQNNGLAFISLKPWSERVGEENSVTAIIQRAMIALSSINKAVVFPFNLPAVAELGTASGFDMELLDNGNLGHEKLTQARNELLSLAAQSPNQVTGVRPNGLEDTPMFKVNVNAAKAEAMGVALSDINQTISTAFGSSYVNDFLNQGRVKKVYVQAGTPFRMLPDNINQWYVRNASGTMAPLSAYSSTEWTYGSPRLERYNGIPSMEILGEAAAGKSTGDAMKFMADLVAKLPAGVGYSWTGLSYQEALSSNQAPALYAISLVVVFLALAALYESWSIPFSVMLVVPLGVVGALLATDLRGLSNDVYFQVGLLTTIGLSAKNAILIVEFAVEMMQKEGKTPIEAIIEAARMRLRPILMTSLAFILGVLPLVISHGAGSGAQNAVGTGVMGGMFAATVLAIYFVPVFFVVVEHLFARFKKAASGENLYFQSLEHHHHHH

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PHOSPHATIDYLETHANOLAMINE
formula_weight	734.0 kDa
src_method	syn
entity_count	21

Entity 3 non-polymer

description	DODECANE
formula_weight	170.3 kDa
src_method	syn
entity_count	7

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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	583735

fit	/app/data/saxs_computation/qp/9qpr/9qpr.fit
pddf	/app/data/pr_computation/qp/9qpr/9qpr.pr.out
profile	/app/data/saxs_computation/qp/9qpr/9qpr.dat