SAXSdb — 9qks

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1. Structure Basics

entry_id	9qks
deposition_date	2025-03-20
title	B subtilis Type VIIb Core Unit (T7bCU) + DUF
keywords	T7SS, Type VII Secretion System, T7bCU, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	41.66 Å
rg_electron	41.11 Å
i0	413463000.00
molecular_weight	168870.0 kDa
excluded_volume	212550 Å³
envelope_volume	318590 Å³
shell_volume	64636 Å³
envelope_diameter	150.3 Å
shell_rg	46.72 Å
envelope_rg	40.68 Å
shape_rg	41.10 Å
total_rg	41.49 Å
total_atoms	11940
n_residues	1441
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	41.51 Å
rg_real_error	0.96 Å
i0_real	4.1350e+08
i0_real_error	6.9320e+06
rg_reciprocal	41.66 Å
i0_reciprocal	413500000.0000
total_estimate	0.8844
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.1 Å
skewness	0.186
kurtosis	-0.385
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	76780000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	ESX secretion system protein YukD
formula_weight	9277.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11940

MGMYIDITIDLKHYNGSVFDLRLSDYHPVKKVIDIAWQAQSVSMPPREGHWIRVVNKDKVFSGECKLSDCGITNGDRLEIL

Source

organism	Bacillus subtilis subsp. subtilis str. 168
ncbi_taxonomy_id	224308
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	ESX secretion system protein YukC
formula_weight	53225.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MSGEQKSYLENQLEAVAEKTDAGYTFTFQREKIKLLDGLEANVIKDINPFFHKEIDVTDDEVIITIQPPSSYKAFRFMKAKDKKSKWQFAYQLVQAVQQHNLSRLNLIVAPENIVFDKGLTPYFLHYGVKESIPPYERDEERVWQELKAAAALAVDGAFAFEDYLKFNETLTFSAEAKAILDAESYDDLLELIQTHIDELEAKAKTYIHIPRKKWNIQRYIGLGLIVLLVPALIYSMYALFFAQPKHQAIVDSNRAFLNKQYSEVISTLSKYDAESLPESVQYQLATSYVEVENLGSAKTKNIENNLVTLQSDPQHFLYWIDYGRGEYKEAISIGRKLEYNDYIYFALAKYKQQLLSEDTNDEDIQKELDSVNSELEKAQKERQENKQSNSETSLVDTSEEQTQTDEEKQAEEKAAEEKAAAEEKAKKEEQKEKEDEKKETEKKDEKKDDKDYKDDDDK

Source

organism	Bacillus subtilis subsp. subtilis str. 168
ncbi_taxonomy_id	224308
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	ESX secretion system protein YukB,Green fluorescent protein
formula_weight	143109.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

MLPFGRKGVRHLSLLWVFYQNNVQKLNLSNLPSSHPVTIGPDVKDSVTISTIPFNSGVISLKRKESGGQYEVFLGNDCLGTIETDISFTLQTDQQDIRLILTGSEPEKSVYFTGNRDEIVCSSEKTNADIYLNPQDFAFAEQSTFSLLRAGGSWSVRPESGTIFLNGEKINANTPLKPGDEIFWNFTQMRVTEQDLLEIVHYAQFETALTETVKPSTEMQKKYPQYRRTPRMVYDLPDDRVSFSFPSQESDQTNRGLWLVILPPLVMLIVMGVVAIIQPRGIFILVSLAMFMMTLITSTVQYFRDKNQRKKREEKRERVYKLYLDNKRKELQALAEKQKQVLEFHFPSFEQMKYLTSEISDRIWEKSLESKDYLQLRLGTGTVPSSYEINMSGGDLANRDIDDLMEKSQHMQRVYKDIRNAPVTVDLAEGPMGLVGKSQIVKNEIHQLIGQLSFFNSYHDLRFVFIFHEEEYKDWEWMKWLPQFQMPHIYAKGFIYNEQTRDQLLSSLYELIRERDLEDDKEKLQFKPHFVFVITNQQLISEHVILEYLEGQHEHLGISTIVAAETKESLSENITTLVRYINEHEGDILIQKKKAVRIPFRLDHHQREDNERFSRTLRTLNHQVGITNSIPETVSFLELFHAKEVKEIGIQQRWLTSESSKSLSVPIGYKGKDDIVYLNLHEKAHGPHGLLAGTTGSGKSEFLQTYILSLAVHFHPHEAAFLLIDYKGGGMAQPFRNIPHLLGTITNIEGSKNFSMRALASIKSELKKRQRLFDQYQVNHINDYTKLYKQGKAEVAMPHLFLISDEFAELKSEEPDFIRELVSAARIGRSLGVHLILATQKPGGIIDDQIWSNSRFKVALKVQDATDSKEILKNSDAANITVTGRGYLQVGNNEVYELFQSAWSGAPYLEEVYGTEDEIAIVTDTGLIPLSEVDTEDNAKKDVQTEIEAVVDEIERIQDEMGIEKLPSPWLPPGAGGLVPRGSGGSGSVDSTESLFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTITFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITGGSGGSGSRGRSGSGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKKG

Source

organism	Bacillus subtilis subsp. subtilis str. 168
ncbi_taxonomy_id	224308
host_organism	Escherichia coli BL21(DE3)

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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	3.80 Å
resolution_method	—
num_particles	303198

fit	/app/data/saxs_computation/qk/9qks/9qks.fit
pddf	/app/data/pr_computation/qk/9qks/9qks.pr.out
profile	/app/data/saxs_computation/qk/9qks/9qks.dat

B subtilis Type VIIb Core Unit (T7bCU) + DUF

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)