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9tfy

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha1 - beta1 complex bound to inositol hexakisphosphate (InsP6)

Method: X-RAY DIFFRACTION D_max: 147.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tfy
deposition_date	2025-11-27
last_revision	2025-12-17
title	Arabidopsis thaliana Casein Kinase 2 (CK2) alpha1 - beta1 complex bound to inositol hexakisphosphate (InsP6)
keywords	protein kinase, inositol polyphosphate, inositol pyrophosphate, flowering time regulation, plant growth, CELL CYCLE; CELL CYCLE
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	46.53 Å
rg_electron	47.23 Å
i0	226339000.00
molecular_weight	123980.0 kDa
excluded_volume	155100 Å³
envelope_volume	216450 Å³
shell_volume	41716 Å³
envelope_diameter	157.2 Å
shell_rg	45.25 Å
envelope_rg	46.59 Å
shape_rg	47.28 Å
total_rg	46.97 Å
total_atoms	8716
n_residues	1052
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	147.9 Å
rg_real	47.82 Å
rg_real_error	0.58 Å
i0_real	2.2430e+08
i0_real_error	2.9890e+06
rg_reciprocal	46.54 Å
i0_reciprocal	226100000.0000
total_estimate	0.6053
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.8 Å
skewness	0.487
kurtosis	-0.674
angular_range	— – 0.1700 Å⁻¹
current_alpha	2.1680
highest_alpha	14220000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.765; Stabil: 0.961; Sysdev: 0.000; Positv: 1.000; Valcen: 0.681; Smooth: 0.010

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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-1
formula_weight	40603.6 kDa
ec_number	2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8722

MSKARVYTEVNVIRPKDYWDYESLIVQWGEQDDYEVVRKVGRGKYSEVFEGINVNSKEKCIIKILKPVKKKKIRREIKILQNLCGGPNIVKLLDVVRDQHSKTPSLIFEYVNSTDFKVLYPTLTDYDIRYYIYELLKALDFCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNQDQLVKIAKVLGTDELNAYLNKYQLELDPQLEALVGRHSRKPWSKFINADNQHLVSPEAIDFLDKLLRYDHQDRLTAKEAMAHAYFAQVRAAETSRMRSQAAALEHHHHHH

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 2 polymer

description	Casein kinase II subunit beta-1
formula_weight	22358.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MDGEDTSWISWFCNLRGNEFFCEVDDDYIQDDFNLCGLSSLVPYYEYALDLILDVESSQGEMFTEEQNELIESAAEMLYGLIHARYILTSKGLAAMLDKYKNYDFGRCPRVYCCGQPCLPVGQSDLPRSSTVKIYCPKCEDIYYPRSKYQGNIDGAYFGTTFPHLFLMTYGHLKPAKATQNYVQRVFGFKLHKP

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 3 non-polymer

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (2)

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length_a	210.189 Å
length_b	210.189 Å
length_c	272.599 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	I 41 2 2
int_tables_number	98
crystal_system	—

resolution	5.500 Å
resolution_low	40.070 Å
r_factor	0.2487
r_work	0.2477
r_free	0.2672

fit	/app/data/saxs_computation/tf/9tfy/9tfy.fit
pddf	/app/data/pr_computation/tf/9tfy/9tfy.pr.out
profile	/app/data/saxs_computation/tf/9tfy/9tfy.dat

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha1 - beta1 complex bound to inositol hexakisphosphate (InsP6)

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 non-polymer

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)