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9vnq

Bacillus Subtilis Ku core homodimer complexed with double strand DNA

Method: ELECTRON MICROSCOPY D_max: 126.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vnq
deposition_date	2025-06-30
title	Bacillus Subtilis Ku core homodimer complexed with double strand DNA
keywords	Non homologous end joining, DNA bridging, DNA BINDING PROTEIN; DNA BINDING 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	38.14 Å
rg_electron	38.44 Å
i0	272669000.00
molecular_weight	122800.0 kDa
excluded_volume	148860 Å³
envelope_volume	210810 Å³
shell_volume	46744 Å³
envelope_diameter	125.5 Å
shell_rg	43.10 Å
envelope_rg	38.13 Å
shape_rg	38.44 Å
total_rg	38.71 Å
total_atoms	8559
n_residues	967
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	126.0 Å
rg_real	38.31 Å
rg_real_error	0.94 Å
i0_real	2.7270e+08
i0_real_error	4.2240e+06
rg_reciprocal	38.21 Å
i0_reciprocal	272600000.0000
total_estimate	0.8690
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.9 Å
skewness	0.389
kurtosis	-0.620
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	52060000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.881

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Non-homologous end joining protein Ku
formula_weight	26052.7 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8559

MHTMWKGSISFGLVNIPIKLYAATEDKDIKLRSLHKEDHAPIKYEKVCTNCEKTLSPDEIVKGYEYVKGKYVVLTDEDLKSLKQEHEEKAVEIVDFVQLQEIDPIYFNRSYFVGPGDNGTKAYTLLREALRSTGKIGIANMTIRSKQQLAILRVYENCIVMESIHYPDEVRSAAQVPGVPDQSNVNDKELQTAITLIDELTAKFEPEKYEDTYRQALLQRVNDKLEN

Source

organism	Bacillus subtilis
ncbi_taxonomy_id	1423
host_organism	Escherichia coli

Entity 2 polymer

description	DNA (31-MER)
formula_weight	9616.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

CTGTAGAAGGTACCTGTAGAAGGTACCTGTA

Entity 3 polymer

description	DNA (31-MER)
formula_weight	9447.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	F

TACAGGTACCTTCTACAGGTACCTTCTACAG

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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	2.74 Å
resolution_method	—
num_particles	156247

fit	/app/data/saxs_computation/vn/9vnq/9vnq.fit
pddf	/app/data/pr_computation/vn/9vnq/9vnq.pr.out
profile	/app/data/saxs_computation/vn/9vnq/9vnq.dat

Bacillus Subtilis Ku core homodimer complexed with double strand DNA

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

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)