SAXSdb — 1cki

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

CASEIN KINASE I DELTA

Rattus norvegicus

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 1–317 Chain B； UniProt 1–317	Mutation：C-TERMINAL TRUNCATION MUTANT CONTAINING RESIDUES 1 - 317	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：MOLECULE: RECOMBINANT CASEIN KINASE I DELTA. CRYSTALS WERE GROWN BY THE SITTING DROP TECHNIQUE, MIXING 3 MICROLITER OF PROTEIN SOLUTION WITH 3 MICROLITER OF RESERVOIR SOLUTION. THE PROTEIN SOLUTION CONSISTED OF 14 MG/ML PROTEIN IN 50 MM TRIS-HCL (PH=7.5), 1 MM EDTA, 5 MM DTT, 0.2 M NACL, 2.5 MM BETA-OCTYL GLUCOSIDE. THE RESERVOIR SOLUTION CONTAINED 15% PEG 3400, 50 MM SODIUM CITRATE, 50 MM DIBASIC POTASSIUM PHOSPHATE, (PH=6.8). ROOM TEMPERATURE.	Resolution 2.30 Å R-free 0.279

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 1CKI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CKJ CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317 COMPLEX WITH BOUND TUNGSTATE Deposited 1995-08-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Mutation：C-TERMINAL TRUNCATION MUTANT CONTAINING RESIDUES 1 - 317 Mutation：C-TERMINAL TRUNCATION MUTANT CONTAINING RESIDUES 1 - 317	WO4 TUNGSTATE(VI)ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions MOLECULE: RECOMBINANT CASEIN KINASE I DELTA. CRYSTALS WERE GROWN BY THE SITTING DROP TECHNIQUE, MIXING 3 MICROLITER OF PROTEIN SOLUTION WITH 3 MICROLITER OF RESERVOIR SOLUTION. THE PROTEIN SOLUTION CONSISTED OF 14 MG/ML PROTEIN IN 50 MM TRIS-HCL (PH=7.5), 1 MM EDTA, 5 MM DTT, 0.2 M NACL, 2.5 MM BETA-OCTYL GLUCOSIDE. THE RESERVOIR SOLUTION CONTAINED 15% PEG 3400, 50 MM SODIUM CITRATE, 50 MM DIBASIC POTASSIUM PHOSPHATE, (PH=6.8). DATA WAS COLLECTED ON A CRYSTAL SOAKED FOR 6 DAYS IN 15% PEG 3400, 50 MM SODIUM CITRATE, 17.5 MM SODIUM TUNGSTATE, (PH=6.8). ROOM TEMPERATURE.	Resolution 2.46 Å R-free 0.271

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KC1D_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 1–317 Author chain B； PDBConstruct 1–317； UniProt 1–317

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cki
Deposition date deposition_date	1995-08-25
Structure title title	RECOMBINANT CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317
Keywords keywords	PROTEIN KINASE, PHOSPHOTRANSFERASE; PHOSPHOTRANSFERASE
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	28.80 Å
Radius of gyration Rg (electron density) rg_electron	28.10 Å
Forward intensity I(0) i0	70523400.00
Molecular weight molecular_weight	67116.0 kDa
Excluded volume excluded_volume	84527 Å³
Envelope volume envelope_volume	103690 Å³
Hydration-shell volume shell_volume	31414 Å³
Envelope diameter envelope_diameter	106.3 Å
Shell Rg shell_rg	34.74 Å
Envelope Rg envelope_rg	28.43 Å
Shape Rg shape_rg	28.06 Å
Total Rg total_rg	28.91 Å
Total atoms total_atoms	4726
Residues n_residues	578
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	99.3 Å
Rg (real space) rg_real	28.85 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	7.0520e+07
I(0) uncertainty (real space) i0_real_error	1.0820e+06
Rg (reciprocal space) rg_reciprocal	28.83 Å
I(0) (reciprocal space) i0_reciprocal	70520000.0000
Solution quality estimate total_estimate	0.8699
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.7 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.371
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16140000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.896; Smooth: 0.981

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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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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ckia_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d1ckib_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (4 domains)

Domain ID domain_id	1ckiA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	1ckiA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	1ckiB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	1ckiB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (3)

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Unit-cell length a length_a	106.840 Å
Unit-cell length b length_b	115.470 Å
Unit-cell length c length_c	60.600 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2790

Description description	CASEIN KINASE I DELTA
Molecular weight formula_weight	36995.5 kDa
EC 编号 ec_number	2.7.1.-
Mutation mutation	C-TERMINAL TRUNCATION MUTANT CONTAINING RESIDUES 1 - 317
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4823

RECOMBINANT CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317

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

CASEIN KINASE I DELTA

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	97

fit	/app/data/saxs_computation/ck/1cki/1cki.fit
pddf	/app/data/pr_computation/ck/1cki/1cki.pr.out
profile	/app/data/saxs_computation/ck/1cki/1cki.dat