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9v5m

The crystal structure of RBBP4-H3 complex

Method: X-RAY DIFFRACTION D_max: 72.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v5m
deposition_date	2025-05-26
last_revision	2026-06-03
title	The crystal structure of RBBP4-H3 complex
keywords	Histone-binding protein, PROTEIN BINDING; PROTEIN BINDING
method	X-RAY DIFFRACTION

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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	22.37 Å
rg_electron	21.19 Å
i0	37741300.00
molecular_weight	46028.0 kDa
excluded_volume	56933 Å³
envelope_volume	67606 Å³
shell_volume	25849 Å³
envelope_diameter	75.6 Å
shell_rg	28.81 Å
envelope_rg	21.62 Å
shape_rg	21.19 Å
total_rg	22.12 Å
total_atoms	3251
n_residues	415
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	72.2 Å
rg_real	22.27 Å
rg_real_error	0.38 Å
i0_real	3.7740e+07
i0_real_error	4.6310e+05
rg_reciprocal	22.30 Å
i0_reciprocal	37740000.0000
total_estimate	0.8873
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.3 Å
skewness	0.234
kurtosis	-0.313
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	8308000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.971

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Histone-binding protein RBBP4
formula_weight	47709.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3520

MADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGTHTSDEQNHLVIASVQLPNDADQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRARYMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNCLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLSKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSVDPEGQGS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Histone H3.3C
formula_weight	1494.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

ARTKQTARKSTGGK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	synthetic construct

Entity 3 non-polymer

description	BIOTIN
formula_weight	244.3 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	269

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6. Citations (1)

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length_a	96.010 Å
length_b	77.463 Å
length_c	64.301 Å
angle_alpha	90.00 °
angle_beta	90.61 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.100 Å
resolution_low	38.730 Å
r_factor	0.1692
r_work	0.1670
r_free	0.2109

fit	/app/data/saxs_computation/v5/9v5m/9v5m.fit
pddf	/app/data/pr_computation/v5/9v5m/9v5m.pr.out
profile	/app/data/saxs_computation/v5/9v5m/9v5m.dat

The crystal structure of RBBP4-H3 complex

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

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)