SAXSdb — 9rgb

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1. Structure Basics

entry_id	9rgb
deposition_date	2025-06-06
last_revision	2025-08-13
title	M.tuberculosis MmpS5L5-acpM complex
keywords	Drug efflux, RND transporter, Tuberculosis, 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	46.13 Å
rg_electron	45.02 Å
i0	977922000.00
molecular_weight	275830.0 kDa
excluded_volume	352610 Å³
envelope_volume	496650 Å³
shell_volume	89145 Å³
envelope_diameter	137.8 Å
shell_rg	52.74 Å
envelope_rg	43.54 Å
shape_rg	45.06 Å
total_rg	45.22 Å
total_atoms	19410
n_residues	2540
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	139.5 Å
rg_real	45.74 Å
rg_real_error	0.81 Å
i0_real	9.7790e+08
i0_real_error	1.6360e+07
rg_reciprocal	46.12 Å
i0_reciprocal	978400000.0000
total_estimate	0.6894
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	65.6 Å
skewness	-0.030
kurtosis	-0.590
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	139100000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.965; Smooth: 0.882

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Siderophore export accessory protein MmpS5
formula_weight	15348.5 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	19410

MSIGTLKRAWIPLLILVVVAIAGFTVQRIRTFFGSEGILVTPKVFADDPEPFDPKVVEYEVSGSGSYVNINYLDLDAKPQRIDGAALPWSLTLKTTAPSAAPNILAQGDGTSITCRITVDGEVKDERTATGVDALTYCFVKSA

Source

organism	Mycobacterium tuberculosis
ncbi_taxonomy_id	1773
host_organism	Mycolicibacterium smegmatis MC2 155

Entity 2 polymer

description	Siderophore exporter MmpL5,Green fluorescent protein
formula_weight	111448.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F

MIVQRTAAPTGSVPPDRHAARPFIPRMIRTFAVPIILGWLVTIAVLNVTVPQLETVGQIQAVSMSPDAAPSMISMKHIGKVFEEGDSDSAAMIVLEGQRPLGDAAHAFYDQMIGRLQADTTHVQSLQDFWGDPLTATGAQSSDGKAAYVQVKLAGNQGESLANESVEAVKTIVERLAPPPGVKVYVTGSAALVADQQQAGDRSLQVIEAVTFTVIIVMLLLVYRSIITSAIMLTMVVLGLLATRGGVAFLGFHRIIGLSTFATNLLVVLAIAAATDYAIFLIGRYQEARGLGQDRESAYYTMFGGTAHVVLGSGLTIAGATFCLSFTRLPYFQTLGVPLAIGMVIVVAAALTLGPAIIAVTSRFGKLLEPKRMARVRGWRKVGAAIVRWPGPILVGAVALALVGLLTLPGYRTNYNDRNYLPADLPANEGYAAAERHFSQARMNPEVLMVESDHDMRNSADFLVINKIAKAIFAVEGISRVQAITRPDGKPIESFYLPPEVFDNPDFQRGLEQFLSPDGHAVRFIISHEGDPMSQAGIARIAKIKTAAKEAIKGTPLEGSAIYLGGTAAMFKDLSDGNTYDLMIAGISALCLIFIIMLITTRSVVAAAVIVGTVVLSLGASFGLSVLIWQHILGIELHWLVLAMAVIILLAVGADYNLLLVARLKEEIHAGINTGIIRAMGGSGSVVTAAGLVFAFTMMSFAVSELTVMAQVGTTIGMGLLFDTLIVRSFMTPSIAALLGKWFWWPQVVRQRPIPQPWPSPASARTFALVALEVLFQGPQFSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYKTSDYKDDDDK

Source

organism	Aequorea victoria
common_name	Water jellyfish, Mesonema victoria
ncbi_taxonomy_id	6100
host_organism	Mycolicibacterium smegmatis MC2 155

Entity 3 polymer

description	Meromycolate extension acyl carrier protein
formula_weight	11084.2 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	G,H,I

MAATQEEIIAGLAEIIEEVTGIEPSEVTPEKSFVDDLDIDXLSMVEIAVQTEDKYGVKIPDEDLAGLRTVGDVVAYIQKLEEENPEAAAALREKFAADQ

Entity 4 non-polymer

description	(1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
formula_weight	746.0 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	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	33185

fit	/app/data/saxs_computation/rg/9rgb/9rgb.fit
pddf	/app/data/pr_computation/rg/9rgb/9rgb.pr.out
profile	/app/data/saxs_computation/rg/9rgb/9rgb.dat

M.tuberculosis MmpS5L5-acpM 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

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)