12sa

Crystal Structure of the Catalytic Subunit of the Circadian Regulator Casein Kinase 2 from Neurospora crassa

Method: X-RAY DIFFRACTION D_max: 119.9 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Casein kinase II subunit alpha

Neurospora crassa

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 2–336 Chain B； UniProt 2–336 Chain C； UniProt 2–336 Chain D； UniProt 2–336 Chain E； UniProt 2–336 Chain F； UniProt 2–336	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M BES-Triethanolamine 10% w/v PEG 8000, 20% v/v 1,5-Pentanediol 0.001M Rubidium chloride 0.001M Strontium acetate 0.001M Cesium acetate 0.001M Barium acetate	Resolution 2.80 Å R-free 0.244

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CSK2A_NEUCR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–338； UniProt 2–336 Author chain B； PDBConstruct 4–338； UniProt 2–336 Author chain C； PDBConstruct 4–338； UniProt 2–336 Author chain D； PDBConstruct 4–338； UniProt 2–336 Author chain E； PDBConstruct 4–338； UniProt 2–336 Author chain F； PDBConstruct 4–338； UniProt 2–336

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	12sa
Deposition date deposition_date	2026-04-16
最后修订 last_revision	2026-04-29
Structure title title	Crystal Structure of the Catalytic Subunit of the Circadian Regulator Casein Kinase 2 from Neurospora crassa
Keywords keywords	Neurospora crassa, Central circadian clock regulator, Casein kinase II, FRQ phosphorylation, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.96 Å
Radius of gyration Rg (electron density) rg_electron	38.84 Å
Forward intensity I(0) i0	687985000.00
Molecular weight molecular_weight	220960.0 kDa
Excluded volume excluded_volume	278980 Å³
Envelope volume envelope_volume	367920 Å³
Hydration-shell volume shell_volume	76303 Å³
Envelope diameter envelope_diameter	126.1 Å
Shell Rg shell_rg	47.02 Å
Envelope Rg envelope_rg	37.75 Å
Shape Rg shape_rg	38.84 Å
Total Rg total_rg	39.31 Å
Total atoms total_atoms	15639
Residues n_residues	1877
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	119.9 Å
Rg (real space) rg_real	39.57 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	6.8800e+08
I(0) uncertainty (real space) i0_real_error	1.0820e+07
Rg (reciprocal space) rg_reciprocal	39.82 Å
I(0) (reciprocal space) i0_reciprocal	688200000.0000
Solution quality estimate total_estimate	0.8853
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.0 Å
Skewness Skewness skewness	0.037
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	142600000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.850

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	84.177 Å
Unit-cell length b length_b	106.752 Å
Unit-cell length c length_c	137.292 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	46.200 Å
R factor r_factor	0.2173
R_work r_work	0.2159
R_free r_free	0.2439

Description description	Casein kinase II subunit alpha
Molecular weight formula_weight	39836.3 kDa
EC 编号 ec_number	2.7.11.1
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15691

Crystal Structure of the Catalytic Subunit of the Circadian Regulator Casein Kinase 2 from Neurospora crassa

1. Protein Identity and Related Structures Protein Identity & Related Structures

Casein kinase II subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Neurospora crassa
NCBI Class编号 ncbi_taxonomy_id	5141
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	46

fit	/app/data/saxs_computation/2s/12sa/12sa.fit
pddf	/app/data/pr_computation/2s/12sa/12sa.pr.out
profile	/app/data/saxs_computation/2s/12sa/12sa.dat