SAXSdb — 3eed

▼

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

Casein kinase II subunit beta

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–193 Chain B； UniProt 1–193	Fragment：regulatory subunit, UNP residues 1-193	ZN ZINC ION × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；25.5% PEG 8000, 15% glycerol, 0.17M ammonium sulfate, 0.085M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.216
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–193 Chain B； UniProt 1–193	Fragment：regulatory subunit, UNP residues 1-193	ZN ZINC ION × 4 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.3；293 K；25.5% PEG 8000, 15% glycerol, 0.17M ammonium sulfate, 0.085M sodium cacodylate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.216

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.

Other PDB	Difference from Current Entry 3EED	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DS5 DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THE TETRAMERIC PROTEIN KINASE CK2 HOLOENZYME. Deposited 2000-01-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 181–203（23 aa） Fragment：RESIDUES 181-203 Chain F 181–203（23 aa） Fragment：RESIDUES 181-203	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, tris-HCl, magnesium chloride, ATP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.16 Å R-free 0.289
1DS5 DIMERIC CRYSTAL STRUCTURE OF THE ALPHA SUBUNIT IN COMPLEX WITH TWO BETA PEPTIDES MIMICKING THE ARCHITECTURE OF THE TETRAMERIC PROTEIN KINASE CK2 HOLOENZYME. Deposited 2000-01-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 181–203（23 aa） Fragment：RESIDUES 181-203 Chain H 181–203（23 aa） Fragment：RESIDUES 181-203	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 2 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；PEG 4000, sodium acetate, tris-HCl, magnesium chloride, ATP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.16 Å R-free 0.289
1JWH Crystal Structure of Human Protein Kinase CK2 Holoenzyme Deposited 2001-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–215（215 aa） Chain D 1–215（215 aa）	Not recorded	PO4 PHOSPHATE ION × 7 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；285 K；initial composition of the drop: 3 ul rhCK2 stock solution [5 mg/ml enzyme in 25 mM Tris/HCl, 300 mM NaCl, 1 mM dithiothreitole, pH 8.5], 1.5 ul reservoir solution [20 % (w/v) PEG3350, 200 mM dipotassium hydrogenphosphate], 3 ul 1 mM adenylyl imidodiphosphate (AMPPNP), 3 ul 2 mM magnesium chloride, 2 ul 10 % (w/v) polyethylene glycol 400 dodecylether (Thesit), pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 285K	Resolution 3.10 Å R-free 0.338
1QF8 TRUNCATED FORM OF CASEIN KINASE II BETA SUBUNIT (2-182) FROM HOMO SAPIENS Deposited 1999-04-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（182 aa） Fragment：BETA SUBUNIT (RESIDUES 1-182) Chain B 1–182（182 aa） Fragment：BETA SUBUNIT (RESIDUES 1-182)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；281 K；CRYSTALS OF CK2 BETA (1-182) WERE GROWN AT 281 K IN 4 MICROLITER SITTING DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN SOLUTION (18 MG/ML) IN 10 MM TRIS (PH 7) AND RESERVOIR SOLUTION WITH 15% PEG 5K MME, 500 MM NACL, 460 MM MGCL2 3% DIOXANE, pH 9, VAPOR DIFFUSION, SITTING DROP	Resolution 1.74 Å R-free 0.219
4DGL Crystal Structure of the CK2 Tetrameric Holoenzyme Deposited 2012-01-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–215（215 aa） Chain B 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；PEG 3350 18%, 0.2 M sodium malonate, pH 7, vapor diffusion, temperature 293K	Resolution 3.00 Å R-free 0.222
4MD7 Crystal Structure of full-length symmetric CK2 holoenzyme Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–215（215 aa） Chain B 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.10 Å R-free 0.263
4MD7 Crystal Structure of full-length symmetric CK2 holoenzyme Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–215（215 aa） Chain D 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.10 Å R-free 0.263
4MD8 Crystal Structure of full-length symmetric CK2 holoenzyme with mutated alpha subunit (F121E) Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–215（215 aa） Chain B 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.30 Å R-free 0.249
4MD8 Crystal Structure of full-length symmetric CK2 holoenzyme with mutated alpha subunit (F121E) Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–215（215 aa） Chain D 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.30 Å R-free 0.249
4MD9 Crystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336) Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–215（215 aa） Chain B 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.50 Å R-free 0.259
4MD9 Crystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336) Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–215（215 aa） Chain D 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.50 Å R-free 0.259
4MD9 Crystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336) Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 1–215（215 aa） Chain O 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.50 Å R-free 0.259
4MD9 Crystal Structure of symmetric CK2 holoenzyme with mutated alpha subunit (F121E truncated at aa 336) Deposited 2013-08-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 1–215（215 aa） Chain J 1–215（215 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；20% PEG3350, 0.2 M ammonium citrate, pH 6.5, VAPOR DIFFUSION, temperature 277K	Resolution 3.50 Å R-free 0.259
4NH1 Crystal structure of a heterotetrameric CK2 holoenzyme complex carrying the Andante-mutation in CK2beta and consistent with proposed models of autoinhibition and trans-autophosphorylation Deposited 2013-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–215（215 aa） Chain D 1–215（215 aa）	Mutation：Met166Ile Mutation：Met166Ile	MG MAGNESIUM ION × 4 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 GOL GLYCEROL × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.30 Å R-free 0.251

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CSK2B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–193； UniProt 1–193 Author chain B； PDBConstruct 1–193； UniProt 1–193

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3eed
Deposition date deposition_date	2008-09-04
Structure title title	Crystal structure of human protein kinase CK2 regulatory subunit (CK2beta; mutant 1-193)
Keywords keywords	;protein kinase CK2, casein kinase 2, casein kinase II, eukaryotic protein kinases, Phosphoprotein, Wnt signaling pathway, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	26.63 Å
Radius of gyration Rg (electron density) rg_electron	26.30 Å
Forward intensity I(0) i0	32357200.00
Molecular weight molecular_weight	43068.0 kDa
Excluded volume excluded_volume	53395 Å³
Envelope volume envelope_volume	68494 Å³
Hydration-shell volume shell_volume	22872 Å³
Envelope diameter envelope_diameter	92.5 Å
Shell Rg shell_rg	31.77 Å
Envelope Rg envelope_rg	26.78 Å
Shape Rg shape_rg	26.35 Å
Total Rg total_rg	26.77 Å
Total atoms total_atoms	3017
Residues n_residues	366
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

▼

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

Maximum dimension Dmax dmax	88.0 Å
Rg (real space) rg_real	26.83 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	3.2360e+07
I(0) uncertainty (real space) i0_real_error	4.4740e+05
Rg (reciprocal space) rg_reciprocal	26.77 Å
I(0) (reciprocal space) i0_reciprocal	32360000.0000
Solution quality estimate total_estimate	0.8452
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.500
Kurtosis Kurtosis kurtosis	-0.415
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20100000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.793; Smooth: 0.893

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Casein kinase II subunit beta
Molecular weight formula_weight	22492.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3099

MSSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDEELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPMLPIGLSDIPGEAMVKLYCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPANQFVPRLYGFKIH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	82

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3eeda_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.4 — Casein kinase II beta subunit
Family Family family	g.41.4.1 — Casein kinase II beta subunit

Domain ID domain_id	d3eedb_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.4 — Casein kinase II beta subunit
Family Family family	g.41.4.1 — Casein kinase II beta subunit

CATH v4.4 (4 domains)

Domain ID domain_id	3eedA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1820 — protein kinase ck2 holoenzyme, chain C, domain 1
Homologous superfamily homologous superfamily	10 — protein kinase ck2 holoenzyme, chain C, domain 1

Domain ID domain_id	3eedA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3eedB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1820 — protein kinase ck2 holoenzyme, chain C, domain 1
Homologous superfamily homologous superfamily	10 — protein kinase ck2 holoenzyme, chain C, domain 1

Domain ID domain_id	3eedB02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	20 —

▶

8. Citations (2)

▶

Unit-cell length a length_a	116.463 Å
Unit-cell length b length_b	116.463 Å
Unit-cell length c length_c	76.088 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	29.120 Å
R factor r_factor	0.1762
R_work r_work	0.1716
R_free r_free	0.2162

fit	/app/data/saxs_computation/ee/3eed/3eed.fit
pddf	/app/data/pr_computation/ee/3eed/3eed.pr.out
profile	/app/data/saxs_computation/ee/3eed/3eed.dat

Crystal structure of human protein kinase CK2 regulatory subunit (CK2beta; mutant 1-193)

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

Casein kinase II subunit beta

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