SAXSdb — 9rai

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1. Structure Basics

entry_id	9rai
deposition_date	2025-05-20
title	Structure of the S.aureus MecA/ClpC/ClpP degradation system
keywords	protein-quality control, AAA+ unfoldases, peptidases, adaptor proteins, CHAPERONE; CHAPERONE
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	74.39 Å
rg_electron	74.80 Å
i0	10569700000.00
molecular_weight	867480.0 kDa
excluded_volume	1085300 Å³
envelope_volume	1722300 Å³
shell_volume	192880 Å³
envelope_diameter	244.2 Å
shell_rg	72.86 Å
envelope_rg	73.77 Å
shape_rg	74.85 Å
total_rg	74.61 Å
total_atoms	60975
n_residues	7728
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	219.2 Å
rg_real	74.28 Å
rg_real_error	1.03 Å
i0_real	1.0540e+10
i0_real_error	2.0810e+08
rg_reciprocal	73.61 Å
i0_reciprocal	10550000000.0000
total_estimate	0.8440
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	73.1 Å
skewness	0.487
kurtosis	-0.257
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0179
highest_alpha	1320000000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.203

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Adapter protein MecA
formula_weight	28354.2 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	60975

MRIERVDDTTVKLFITYSDIEARGFSREDLWTNRKRGEEFFWSMMDEINEEEDFVVEGPLWIQVHAFEKGVEVTISKSKNEDMMNMSDDDATDQFDEQVQELLAQTLEGEDQLEELFEQRTKEKEAQGSKRQKSSARKNTRTIIVKFNDLEDVINYAYHSNPITTEFEDLLYMVDGTYYYAVYFDSHVDQEVINDSYSQLLEFAYPTDRTEVYLNDYAKIIMSHNVTAQVRRYFPETTE

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 2 polymer

description	unknown substrate
formula_weight	1549.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S

XXXXXXXXXXXXXXXXXX

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 3 polymer

description	ATP-dependent Clp protease ATP-binding subunit ClpC
formula_weight	91170.4 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	a,b,c,d,e,f

MLFGRLTERAQRVLAHAQEEAIRLNHSNIGTEHLLLGLMKEPEGIAAKVLESFNITEDKVIEEVEKLIGHGQDHVGTLHYTPRAKKVIELSMDEARKLHHNFVGTEHILLGLIRENEGVAARVFANLDLNITKARAQVVKALGNPEMSNKNAQASKSNNTPTLDSLARDLTVIAKDGTLDPVIGRDKEITRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQAIVNNEVPETLKDKRVMSLDMGTVVAGTKYRGEFEERLKKVMEEIQQAGNVILFIDELHTLVGAGGAEGAIDASNILKPALARGELQCIGATTLDEYRKNIEKDAALERRFQPVQVDEPSVVDTVAILKGLRDRYEAHHRINISDEAIEAAVKLSNRYVSDRFLPDKAIDLIDEASSKVRLKSHTTPNNLKEIEQEIEKVKNEKDAAVHAQEFENAANLRDKQTKLEKQYEEAKNEWKNAQNGMSTSLSEEDIAEVIAGWTGIPLTKINETESEKLLSLEDTLHERVIGQKDAVNSISKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFGDDDAMIRVDMSEFMEKHAVSRLVGAPPGYVGHDDGGQLTEKVRRKPYSVILFDEIEKAHPDVFNILLQVLDDGHLTDTKGRTVDFRNTIIIMTSNVGAQELQDQRFAGFGGSSDGQDYETIRKTMLKELKNSFRPEFLNRVDDIIVFHKLTKEELKEIVTMMVNKLTNRLSEQNINIIVTDKAKDKIAEEGYDPEYGARPLIRAIQKTIEDNLSELILDGNQIEGKKVTVDHDGKEFKYDIAEQTSETKTPSQA

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 4 polymer

description	ATP-dependent Clp protease proteolytic subunit
formula_weight	21536.5 kDa
ec_number	3.4.21.92
src_method	man
entity_count	14

Polymer

type	polypeptide(L)
strand_id	G,H,I,J,K,L,M,N,O,P,Q,R,T,U

MNLIPTVIETTNRGERAYDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPETK

Source

organism	Staphylococcus aureus
ncbi_taxonomy_id	1280
host_organism	Escherichia coli

Entity 5 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	7

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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	triclinic

resolution	3.00 Å
resolution_method	—
num_particles	82854

fit	/app/data/saxs_computation/ra/9rai/9rai.fit
pddf	/app/data/pr_computation/ra/9rai/9rai.pr.out
profile	/app/data/saxs_computation/ra/9rai/9rai.dat

Structure of the S.aureus MecA/ClpC/ClpP degradation system

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

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)