SAXSdb — 8oyk

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

Isoform 2 of SCL-interrupting locus protein

OrganismNot specified

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 718–749 Chain B； UniProt 718–749	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；277 K；0.9 mM peptide, 50 mM Tris, and 10 % v/v MPD, at pH 8.0.	Resolution 1.90 Å R-free 0.225
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 718–749 Chain E； UniProt 718–749	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；277 K；0.9 mM peptide, 50 mM Tris, and 10 % v/v MPD, at pH 8.0.	Resolution 1.90 Å R-free 0.225
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 718–749 Chain F； UniProt 718–749	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；277 K；0.9 mM peptide, 50 mM Tris, and 10 % v/v MPD, at pH 8.0.	Resolution 1.90 Å R-free 0.225

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 8OYK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4YYP Crystal structure of human PLK4-PB3 in complex with STIL-CC Deposited 2015-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 720–751（32 aa） Fragment：residues 720-751	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Thin needles grew in precipitant solution containing 100 mM Hepes, pH 7.0, 20 mM MgCl2 and 22% Poly(acrylic acid sodium salt) 5100. After extensive optimization and seeding plate-like crystals were grown in a drop consisting of 50% PLK4-PB3/STIL-CC complex solution, 33.3% precipitant solution (100 mM phosphate/citrate pH 4.2, 40% (v/v) Ethanol, 5% (w/v) PEG 1000) and 16.7% of seed stock solution.	Resolution 2.60 Å R-free 0.254
5LHW Central Coiled-Coil Domain of Human STIL Deposited 2016-07-13	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 726–750（25 aa） Fragment：UNP residues 726-750	Not recorded	P6G HEXAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；292 K；150 nl protein solution (58.6 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM TCEP) and 150 nl of mother liquor (7 mM HEPES pH 8.2, 93 mM Tris pH 9.0, 55.36% v/v PEG 550 MME, 10% v/v glycerol)	Resolution 0.91 Å R-free 0.139
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 726–750（25 aa） Fragment：UNP residues 726-750	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 726–750（25 aa） Fragment：UNP residues 726-750	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
5LHZ PB3 Domain of Human PLK4 in Complex with Coiled-Coil Domain of STIL Deposited 2016-07-13	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 726–750（25 aa） Fragment：UNP residues 726-750	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；150nl Protein solution (41.87 mg/ml protein in 20 mM Tris pH 7.5, 150 mM NaCl, 2 mM DTT) and 50 nl mother liquor (100mM MES pH 6.0, 191.7 mM Zn acetate, 10% Isopropanol)	Resolution 2.51 Å R-free 0.282
8OYL Coiled-Coil Domain of Human STIL, Q729L Mutant Deposited 2023-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 718–749（32 aa）	Not recorded	NA SODIUM ION × 4 CD CADMIUM ION × 8 CL CHLORIDE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；293 K；1.5 mM peptide, 50 mM Cadmium chloride hemi(pentahydrate), 50 mM Sodium acetate, and 15 % v/v PEG 400, at pH 4.6	Resolution 1.92 Å R-free 0.190

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STIL_HUMAN
Isoform	Q15468-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–32； UniProt 718–749 Author chain B； PDBConstruct 1–32； UniProt 718–749 Author chain C； PDBConstruct 1–32； UniProt 718–749 Author chain D； PDBConstruct 1–32； UniProt 718–749 Author chain E； PDBConstruct 1–32； UniProt 718–749 Author chain F； PDBConstruct 1–32； UniProt 718–749

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	8oyk
Deposition date deposition_date	2023-05-05
Structure title title	Coiled-Coil Domain of Human STIL, L736E Mutant
Keywords keywords	STIL, coiled coil, dimer, antiparallel, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
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	23.81 Å
Radius of gyration Rg (electron density) rg_electron	24.16 Å
Forward intensity I(0) i0	9336110.00
Molecular weight molecular_weight	21986.0 kDa
Excluded volume excluded_volume	27338 Å³
Envelope volume envelope_volume	35942 Å³
Hydration-shell volume shell_volume	14782 Å³
Envelope diameter envelope_diameter	95.1 Å
Shell Rg shell_rg	26.72 Å
Envelope Rg envelope_rg	24.66 Å
Shape Rg shape_rg	24.16 Å
Total Rg total_rg	24.50 Å
Total atoms total_atoms	1550
Residues n_residues	186
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	64.2 Å
Rg (real space) rg_real	22.02 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	8.8900e+06
I(0) uncertainty (real space) i0_real_error	9.7300e+04
Rg (reciprocal space) rg_reciprocal	24.21 Å
I(0) (reciprocal space) i0_reciprocal	9335000.0000
Solution quality estimate total_estimate	0.6714
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	20.1 Å
Skewness Skewness skewness	0.441
Kurtosis Kurtosis kurtosis	-0.530
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	1.7640
Highest regularization parameter α highest_alpha	1494000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.958; Stabil: 0.991; Sysdev: 0.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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Unit-cell length a length_a	43.539 Å
Unit-cell length b length_b	31.269 Å
Unit-cell length c length_c	64.473 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.08 °
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	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	63.830 Å
R factor r_factor	0.1827
R_work r_work	0.1805
R_free r_free	0.2249

Description description	Isoform 2 of SCL-interrupting locus protein
Molecular weight formula_weight	3834.3 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	1697

Coiled-Coil Domain of Human STIL, L736E Mutant

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

Isoform 2 of SCL-interrupting locus protein

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

fit	/app/data/saxs_computation/oy/8oyk/8oyk.fit
pddf	/app/data/pr_computation/oy/8oyk/8oyk.pr.out
profile	/app/data/saxs_computation/oy/8oyk/8oyk.dat