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9qpt

Single particle cryo-EM structure of MdtF V610F with bound Rhodamine 6G

Method: ELECTRON MICROSCOPY D_max: 139.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpt
deposition_date	2025-03-28
title	Single particle cryo-EM structure of MdtF V610F with bound Rhodamine 6G
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	45.46 Å
rg_electron	44.64 Å
i0	1495190000.00
molecular_weight	342800.0 kDa
excluded_volume	438130 Å³
envelope_volume	568890 Å³
shell_volume	100140 Å³
envelope_diameter	143.7 Å
shell_rg	53.83 Å
envelope_rg	43.98 Å
shape_rg	44.66 Å
total_rg	44.92 Å
total_atoms	24061
n_residues	3054
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	139.6 Å
rg_real	45.19 Å
rg_real_error	0.77 Å
i0_real	1.4950e+09
i0_real_error	2.3560e+07
rg_reciprocal	45.46 Å
i0_reciprocal	1496000000.0000
total_estimate	0.8748
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.9 Å
skewness	0.151
kurtosis	-0.437
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	295900000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.638

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Multidrug resistance protein MdtF
formula_weight	113807.9 kDa
mutation	V610F
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	24061

MANYFIDRPVFAWVLAIIMMLAGGLAIMNLPVAQYPQIAPPTITVSATYPGADAQTVEDSVTQVIEQNMNGLDGLMYMSSTSDAAGNASITLTFETGTSPDIAQVQVQNKLQLAMPSLPEAVQQQGISVDKSSSNILMVAAFISDNGSLNQYDIADYVASNIKDPLSRTAGVGSVQLFGSEYAMRIWLDPQKLNKYNLVPSDVISQIKVQNNQISGGQLGGMPQAADQQLNASIIVQTRLQTPEEFGKILLKVQQDGSQVLLRDVARVELGAEDYSTVARYNGKPAAGIAIKLAAGANALDTSRAVKEELNRLSAYFPASLKTVYPYDTTPFIEISIQEVFKTLVEAIILVFLVMYLFLQNFRATIIPTIAVPVVILGTFAILSAVGFTINTLTMFGMVLAIGLLVDDAIVVVENVERVIAEDKLPPKEATHKSMGQIQRALVGIAVVLSAVFMPMAFMSGATGEIYRQFSITLISSMLLSVFVAMSLTPALCATILKAAPEGGHKPNALFARFNTLFEKSTQHYTDSTRSLLRCTGRYMVVYLLICAGMAVLFLRTPTSFLPEEDQGVFMTTAQLPSGATMVNTTKVLQQVTDYYLTKEKDNVQSVFTFGGFGFSGQGQNNGLAFISLKPWSERVGEENSVTAIIQRAMIALSSINKAVVFPFNLPAVAELGTASGFDMELLDNGNLGHEKLTQARNELLSLAAQSPNQVTGVRPNGLEDTPMFKVNVNAAKAEAMGVALSDINQTISTAFGSSYVNDFLNQGRVKKVYVQAGTPFRMLPDNINQWYVRNASGTMAPLSAYSSTEWTYGSPRLERYNGIPSMEILGEAAAGKSTGDAMKFMADLVAKLPAGVGYSWTGLSYQEALSSNQAPALYAISLVVVFLALAALYESWSIPFSVMLVVPLGVVGALLATDLRGLSNDVYFQVGLLTTIGLSAKNAILIVEFAVEMMQKEGKTPIEAIIEAARMRLRPILMTSLAFILGVLPLVISHGAGSGAQNAVGTGVMGGMFAATVLAIYFVPVFFVVVEHLFARFKKAASGENLYFQSLEHHHHHH

Source

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

Entity 2 non-polymer

description	DODECANE
formula_weight	170.3 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	PHOSPHATIDYLETHANOLAMINE
formula_weight	734.0 kDa
src_method	syn
entity_count	23

Entity 4 non-polymer

description	RHODAMINE 6G
formula_weight	443.6 kDa
src_method	syn
entity_count	1

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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	3.20 Å
resolution_method	—
num_particles	1967418

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