SAXSdb — 1ckj

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

RECOMBINANT 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	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

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 1CKJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CKI RECOMBINANT CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317 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	No recorded non-water small molecule	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

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	1ckj
Deposition date deposition_date	1995-08-25
Structure title title	CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317 COMPLEX WITH BOUND TUNGSTATE
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	28.87 Å
Radius of gyration Rg (electron density) rg_electron	28.25 Å
Forward intensity I(0) i0	80248200.00
Molecular weight molecular_weight	69614.0 kDa
Excluded volume excluded_volume	86532 Å³
Envelope volume envelope_volume	107700 Å³
Hydration-shell volume shell_volume	32401 Å³
Envelope diameter envelope_diameter	106.2 Å
Shell Rg shell_rg	34.86 Å
Envelope Rg envelope_rg	28.56 Å
Shape Rg shape_rg	28.21 Å
Total Rg total_rg	29.02 Å
Total atoms total_atoms	4839
Residues n_residues	589
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	101.5 Å
Rg (real space) rg_real	28.92 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	8.0250e+07
I(0) uncertainty (real space) i0_real_error	1.2720e+06
Rg (reciprocal space) rg_reciprocal	28.90 Å
I(0) (reciprocal space) i0_reciprocal	80250000.0000
Solution quality estimate total_estimate	0.8586
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.420
Kurtosis Kurtosis kurtosis	-0.274
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15620000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.893; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RECOMBINANT 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 Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4871

MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFGASRAADDAERERRDREERLRH

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	TUNGSTATE(VI)ION
Molecular weight formula_weight	247.8 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ckja_
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	d1ckjb_
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	1ckjA01
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	1ckjA02
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	1ckjB01
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	1ckjB02
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	106.740 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	2.460 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1920
R_work r_work	0.1920
R_free r_free	0.2710

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

CASEIN KINASE I DELTA TRUNCATION MUTANT CONTAINING RESIDUES 1-317 COMPLEX WITH BOUND TUNGSTATE

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

RECOMBINANT 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