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9r5k

;Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. ;

Method: ELECTRON MICROSCOPY D_max: 153.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r5k
deposition_date	2025-05-09
title	;Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. ;
keywords	Nucleosome, Remodelling enzyme, 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	44.54 Å
rg_electron	41.73 Å
i0	935194000.00
molecular_weight	183450.0 kDa
excluded_volume	201360 Å³
envelope_volume	332320 Å³
shell_volume	66837 Å³
envelope_diameter	161.5 Å
shell_rg	46.89 Å
envelope_rg	41.57 Å
shape_rg	41.53 Å
total_rg	42.37 Å
total_atoms	22256
n_residues	1066
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	153.7 Å
rg_real	44.56 Å
rg_real_error	1.85 Å
i0_real	9.3520e+08
i0_real_error	1.8970e+07
rg_reciprocal	44.54 Å
i0_reciprocal	935200000.0000
total_estimate	0.8580
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.3 Å
skewness	0.389
kurtosis	-0.048
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	82080000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.805

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DNA (162-MER)
formula_weight	49864.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I
atom_count	22256

CCTATACGCGGGCGCACTGCAGAAGCTTGGTCCCGGGGCCGCTCAATTGGTCGTAGGAAGCTCTAGATCCGCTTAAACGAACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCGAT

Entity 2 polymer

description	DNA (162-MER)
formula_weight	50153.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

ATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTTCGTTTAAGCGGATCTAGAGCTTCCTACGACCAATTGAGCGGCCCCGGGACCAAGCTTCTGCAGTGCGCCCGCGTATAGG

Entity 3 polymer

description	Histone H3.2
formula_weight	15421.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 4 polymer

description	Histone H4
formula_weight	11394.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 5 polymer

description	Histone H2A type 1
formula_weight	13993.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKKTESAKSAKSK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 6 polymer

description	Histone H2B 1.1
formula_weight	13965.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source

organism	Xenopus laevis
common_name	African clawed frog
ncbi_taxonomy_id	8355
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

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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	4.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.20 Å
resolution_method	—
num_particles	135000

fit	/app/data/saxs_computation/r5/9r5k/9r5k.fit
pddf	/app/data/pr_computation/r5/9r5k/9r5k.pr.out
profile	/app/data/saxs_computation/r5/9r5k/9r5k.dat

;Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. ;

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

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)