SAXSdb — 9r2m

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1. Structure Basics

entry_id	9r2m
deposition_date	2025-04-30
title	p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map)
keywords	Tumour-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	54.41 Å
rg_electron	54.05 Å
i0	1319620000.00
molecular_weight	231370.0 kDa
excluded_volume	260030 Å³
envelope_volume	465140 Å³
shell_volume	76100 Å³
envelope_diameter	204.4 Å
shell_rg	51.37 Å
envelope_rg	54.84 Å
shape_rg	54.18 Å
total_rg	53.66 Å
total_atoms	15971
n_residues	1847
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	193.7 Å
rg_real	54.91 Å
rg_real_error	2.42 Å
i0_real	1.3200e+09
i0_real_error	2.7140e+07
rg_reciprocal	53.99 Å
i0_reciprocal	1318000000.0000
total_estimate	0.8074
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.7 Å
skewness	0.627
kurtosis	-0.105
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	127100000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.667; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.558

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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	15971

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	46960.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

ATCCTGGAGAATCCCGGTCTGCAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCAAACATGCCCGGGCATGTCCCTGTGAT

Entity 6 polymer

description	DNA-rev
formula_weight	47499.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCACAGGGACATGCCCGGGCATGTTTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTGCAGACCGGGATTCTCCAGGAT

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	3.50 Å
resolution_method	—
num_particles	163724

fit	/app/data/saxs_computation/r2/9r2m/9r2m.fit
pddf	/app/data/pr_computation/r2/9r2m/9r2m.pr.out
profile	/app/data/saxs_computation/r2/9r2m/9r2m.dat

p53 bound to nucleosome at position SHL+5.9 (non-crosslinked sample, composite map)

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)