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9vno

The crystal structure of the Ehd3 tandem PHD-H3K4me1 complex.

Method: X-RAY DIFFRACTION D_max: 66.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vno
deposition_date	2025-06-30
last_revision	2026-02-04
title	The crystal structure of the Ehd3 tandem PHD-H3K4me1 complex.
keywords	histone modification, histone reader, GENE REGULATION; GENE REGULATION
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	17.46 Å
rg_electron	17.25 Å
i0	5446130.00
molecular_weight	15685.0 kDa
excluded_volume	19110 Å³
envelope_volume	23496 Å³
shell_volume	12454 Å³
envelope_diameter	66.7 Å
shell_rg	22.20 Å
envelope_rg	18.26 Å
shape_rg	17.33 Å
total_rg	17.91 Å
total_atoms	1072
n_residues	131
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	66.4 Å
rg_real	17.60 Å
rg_real_error	0.56 Å
i0_real	5.4460e+06
i0_real_error	6.8010e+04
rg_reciprocal	17.58 Å
i0_reciprocal	5446000.0000
total_estimate	0.7934
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	17.7 Å
skewness	0.561
kurtosis	0.037
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0000
highest_alpha	798300.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.588; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.555; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	PHD finger protein EHD3
formula_weight	15235.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1204

TALSNLCKHCGTCEDDDKRFMVCGHPYCVYKFYHIRCLKTSQLAIEQQKKLGCWYCPSCLCRGCFQDKDDDQIVMCDGCDEGYHIYCMRPARNTIPKGKWYCTFCKIRRAAEGMHKYEDSVLKIHGNSKHA

Source

organism	Oryza sativa subsp. japonica
common_name	Rice
ncbi_taxonomy_id	39947
host_organism	Escherichia coli

Entity 2 polymer

description	Histone H3.2
formula_weight	1321.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

ARTKQTARKSTG

Source

organism	Oryza sativa subsp. japonica
common_name	Rice
ncbi_taxonomy_id	39947
host_organism	Oryza sativa

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	126

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6. Citations (1)

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length_a	74.640 Å
length_b	74.640 Å
length_c	73.616 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	I 41
int_tables_number	80
crystal_system	—

resolution	1.500 Å
resolution_low	26.390 Å
r_factor	0.1624
r_work	0.1616
r_free	0.1776

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

The crystal structure of the Ehd3 tandem PHD-H3K4me1 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)