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9rfn

Structure of protein kinase CK2alpha mutant E264D associated with the Okur-Chung Neurodevelopmental Syndrome

Method: X-RAY DIFFRACTION D_max: 99.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rfn
deposition_date	2025-06-04
last_revision	2026-04-29
title	Structure of protein kinase CK2alpha mutant E264D associated with the Okur-Chung Neurodevelopmental Syndrome
keywords	OCNDS, Okur-CHung neurodeverlopmental syndrome, casein kinase II, protein kinase, CK2, protein kinase CK2, TRANSFERASE; TRANSFERASE
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	30.94 Å
rg_electron	30.25 Å
i0	105569000.00
molecular_weight	80061.0 kDa
excluded_volume	99665 Å³
envelope_volume	125830 Å³
shell_volume	35531 Å³
envelope_diameter	104.1 Å
shell_rg	36.49 Å
envelope_rg	29.92 Å
shape_rg	30.28 Å
total_rg	30.73 Å
total_atoms	5638
n_residues	660
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	99.8 Å
rg_real	30.99 Å
rg_real_error	0.75 Å
i0_real	1.0560e+08
i0_real_error	1.6600e+06
rg_reciprocal	30.97 Å
i0_reciprocal	105600000.0000
total_estimate	0.8887
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.3 Å
skewness	0.367
kurtosis	-0.518
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	30410000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.916

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Casein kinase II subunit alpha
formula_weight	47365.9 kDa
ec_number	2.7.11.1
mutation	E264D
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5836

MGSSHHHHHHSSGLVPRGSHMSGPVPSRARVYTDVNTHRPREYWDYESHVVEWGNQDDYQLVRKLGRGKYSEVFEAINITNNEKVVVKILKPVKKKKIKREIKILENLRGGPNIITLADIVKDPVSRTPALVFEHVNNTDFKQLYQTLTDYDIRFYMYEILKALDYCHSMGIMHRDVKPHNVMIDHEHRKLRLIDWGLAEFYHPGQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGHDNYDQLVRIAKVLGTEDLYDYIDKYNIDLDPRFNDILGRHSRKRWERFVHSENQHLVSPEALDFLDKLLRYDHQSRLTAREAMEHPYFYTVVKDQARMGSSSMPGGSTPVSSANMMSGISSVPTPSPLGPLAGSPVIAAANPLGMPVPAAAGAQQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	nat
entity_count	1

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	12

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	173

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6. Citations (1)

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length_a	128.408 Å
length_b	128.408 Å
length_c	124.512 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	2.580 Å
resolution_low	73.360 Å
r_factor	0.2427
r_work	0.2407
r_free	0.2799

fit	/app/data/saxs_computation/rf/9rfn/9rfn.fit
pddf	/app/data/pr_computation/rf/9rfn/9rfn.pr.out
profile	/app/data/saxs_computation/rf/9rfn/9rfn.dat

Structure of protein kinase CK2alpha mutant E264D associated with the Okur-Chung Neurodevelopmental Syndrome

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