SAXSdb — 9r04

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1. Structure Basics

entry_id	9r04
deposition_date	2025-04-24
title	p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample)
keywords	tumor suppressor, transcription factor, GENE REGULATION; GENE REGULATION
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	51.72 Å
rg_electron	51.05 Å
i0	1300390000.00
molecular_weight	229650.0 kDa
excluded_volume	258170 Å³
envelope_volume	463120 Å³
shell_volume	77872 Å³
envelope_diameter	178.4 Å
shell_rg	51.57 Å
envelope_rg	51.17 Å
shape_rg	51.16 Å
total_rg	50.80 Å
total_atoms	15855
n_residues	1836
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	182.9 Å
rg_real	51.92 Å
rg_real_error	2.15 Å
i0_real	1.3000e+09
i0_real_error	2.6570e+07
rg_reciprocal	51.55 Å
i0_reciprocal	1300000000.0000
total_estimate	0.8472
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.9 Å
skewness	0.479
kurtosis	-0.267
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	108600000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.758; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.741

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Histone H3.1
formula_weight	15719.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	15855

GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H4
formula_weight	11676.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Histone H2A type 1-B/E
formula_weight	14447.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 polymer

description	Histone H2B type 1-J
formula_weight	14088.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 polymer

description	DNA-for
formula_weight	46982.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCCTGGAGAAACATGCCCGGGCATGTCCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGAT

Entity 6 polymer

description	DNA-rev
formula_weight	47471.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGGACATGCCCGGGCATGTTTCTCCAGGAT

Entity 7 polymer

description	Cellular tumor antigen p53
formula_weight	46495.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	K,L,M,N

MDWSHPQFEKSAVDENLYFQGGGRMEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

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6. Citations (1)

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resolution	4.20 Å
resolution_method	—
num_particles	10015

fit	/app/data/saxs_computation/r0/9r04/9r04.fit
pddf	/app/data/pr_computation/r0/9r04/9r04.pr.out
profile	/app/data/saxs_computation/r0/9r04/9r04.dat

p53 bound to the nucleosome at position SHL-5.7 (crosslinked sample)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

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 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)