← Back to search

9tfx

Arabidopsis thaliana Casein Kinase 2 (CK2) alpha isoform 1 in complex with inositol hexakisphosphate (InsP6)

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9tfx
deposition_date	2025-11-27
last_revision	2025-12-10
title	Arabidopsis thaliana Casein Kinase 2 (CK2) alpha isoform 1 in complex with inositol hexakisphosphate (InsP6)
keywords	protein kinase, inositol polyphosphate, inositol pyrophosphate, flowering time regulation, plant growth, CELL CYCLE; CELL CYCLE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	22.17 Å
rg_electron	20.84 Å
i0	27857800.00
molecular_weight	40699.0 kDa
excluded_volume	51026 Å³
envelope_volume	60006 Å³
shell_volume	23742 Å³
envelope_diameter	73.8 Å
shell_rg	28.07 Å
envelope_rg	21.27 Å
shape_rg	20.83 Å
total_rg	21.80 Å
total_atoms	5671
n_residues	337
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

▼

3. P(r) Analysis (GNOM)

dmax	73.2 Å
rg_real	22.07 Å
rg_real_error	0.56 Å
i0_real	2.7860e+07
i0_real_error	4.1610e+05
rg_reciprocal	22.09 Å
i0_reciprocal	27860000.0000
total_estimate	0.8057
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	26.2 Å
skewness	0.238
kurtosis	-0.360
angular_range	— – 0.3600 Å⁻¹
current_alpha	0.0000
highest_alpha	5459000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

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	1

Polymer

type	polypeptide(L)
strand_id	AAAA
atom_count	5913

MSKARVYTEVNVIRPKDYWDYESLIVQWGEQDDYEVVRKVGRGKYSEVFEGINVNSKEKCIIKILKPVKKKKIRREIKILQNLCGGPNIVKLLDVVRDQHSKTPSLIFEYVNSTDFKVLYPTLTDYDIRYYIYELLKALDFCHSQGIMHRDVKPHNVMIDHELRKLRLIDWGLAEFYHPGKEYNVRVASRYFKGPELLVDLQDYDYSLDMWSLGCMFAGMIFRKEPFFYGHDNQDQLVKIAKVLGTDELNAYLNKYQLELDPQLEALVGRHSRKPWSKFINADNQHLVSPEAIDFLDKLLRYDHQDRLTAKEAMAHAYFAQVRAAETSRMRSQAAALEHHHHHH

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli

Entity 2 non-polymer

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	BENZOIC ACID
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	197

▶

6. Citations (2)

▶

length_a	61.903 Å
length_b	63.897 Å
length_c	97.211 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

resolution	1.700 Å
resolution_low	38.690 Å
r_factor	0.2100
r_work	0.2082
r_free	0.2402

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