SAXSdb — 1ygs

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

SMAD4

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 319–552	Fragment：C-TERMINAL DOMAIN, RESIDUES 319 - 552	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；100 MM NAMES, PH6.5, 25% PEG MONOMETHYLETHER 5000, 5 MM DTT, 200 MM (NH4)2SO4	Resolution 2.10 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 1YGS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DD1 CRYSTAL STRUCTURE ANALYSIS OF THE SMAD4 ACTIVE FRAGMENT Deposited 1999-11-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT Chain B 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT Chain C 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT	Not recorded	SO4 SULFATE ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；PEG 4000, LISO4, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.62 Å R-free 0.175
1DD1 CRYSTAL STRUCTURE ANALYSIS OF THE SMAD4 ACTIVE FRAGMENT Deposited 1999-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT Chain B 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT Chain C 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT	Not recorded	SO4 SULFATE ION × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；PEG 4000, LISO4, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.62 Å R-free 0.175
1G88 S4AFL3ARG515 MUTANT Deposited 2000-11-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT Chain B 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT Chain C 285–552（268 aa） Fragment：SMAD4 ACTIVE FRAGMENT	Mutation：R515S Mutation：R515S Mutation：R515S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.00 Å R-free 0.263
1MR1 Crystal Structure of a Smad4-Ski Complex Deposited 2002-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 319–552（234 aa） Fragment：MH2 domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.85 Å R-free 0.280
1MR1 Crystal Structure of a Smad4-Ski Complex Deposited 2002-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 319–552（234 aa） Fragment：MH2 domain	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；dioxane, potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.85 Å R-free 0.280
1U7F Crystal Structure of the phosphorylated Smad3/Smad4 heterotrimeric complex Deposited 2004-08-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 314–552（239 aa） Fragment：MH2 and Linker domains	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；50 mM Tris-HCl, 0-15 mM magnesium chloride, 5-15% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.247
1U7V Crystal Structure of the phosphorylated Smad2/Smad4 heterotrimeric complex Deposited 2004-08-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 314–549（236 aa） Fragment：MH2 and Linker domains	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；50 mM Tris-HCl, 0-15 mM magnesium chloride, 5-15% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.279
5C4V Ski-like protein Deposited 2015-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 314–549（236 aa） Fragment：residues 314-549	Not recorded	GOL GLYCEROL × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5	Resolution 2.60 Å R-free 0.242
5C4V Ski-like protein Deposited 2015-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 314–549（236 aa） Fragment：residues 314-549	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5	Resolution 2.60 Å R-free 0.242
5C4V Ski-like protein Deposited 2015-06-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 314–549（236 aa） Fragment：residues 314-549	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.8-3.3 M sodium chloride, 0.1 M Bis-Tris pH 5.5	Resolution 2.60 Å R-free 0.242
5MEY Crystal structure of Smad4-MH1 bound to the GGCGC site. Deposited 2016-11-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 10–140（131 aa）	Not recorded	ZN ZINC ION × 2 CL CHLORIDE ION × 8 PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 2 CA CALCIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG 6000, 0.2 M NaCl, 0.1 M sodium acetate pH 5.0	Resolution 2.05 Å R-free 0.238
5MEZ Crystal structure of Smad4-MH1 bound to the GGCT site. Deposited 2016-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 10–140（131 aa） Chain B 10–140（131 aa）	Not recorded	ZN ZINC ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；24% PEG 3350, 0.2 M calcium chloride	Resolution 2.98 Å R-free 0.252
5MF0 Crystal structure of Smad4-MH1 bound to the GGCCG site. Deposited 2016-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 10–140（131 aa） Chain B 10–140（131 aa）	Not recorded	ZN ZINC ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；16% PEG MME 2000 and 0.1 M sodium acetate pH 5.0	Resolution 3.03 Å R-free 0.270

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SMA4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 319–552

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	1ygs
Deposition date deposition_date	1997-10-03
Structure title title	CRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN
Keywords keywords	;SMAD4, TUMOR SUPPRESSOR C-TERMINAL DOMAIN, TGF-BETA SIGNAL MEDIATOR, BETA-SANDWICH SCAFFOLD WITH A THREE-HELIX BUNDLE, TUMOUR SUPPRESSOR ;; TUMOUR SUPPRESSOR
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	17.83 Å
Radius of gyration Rg (electron density) rg_electron	16.50 Å
Forward intensity I(0) i0	8966920.00
Molecular weight molecular_weight	21633.0 kDa
Excluded volume excluded_volume	26888 Å³
Envelope volume envelope_volume	30683 Å³
Hydration-shell volume shell_volume	15728 Å³
Envelope diameter envelope_diameter	57.1 Å
Shell Rg shell_rg	22.43 Å
Envelope Rg envelope_rg	16.81 Å
Shape Rg shape_rg	16.48 Å
Total Rg total_rg	17.51 Å
Total atoms total_atoms	1520
Residues n_residues	190
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	58.4 Å
Rg (real space) rg_real	17.75 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	8.9670e+06
I(0) uncertainty (real space) i0_real_error	1.1300e+05
Rg (reciprocal space) rg_reciprocal	17.76 Å
I(0) (reciprocal space) i0_reciprocal	8967000.0000
Solution quality estimate total_estimate	0.8881
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	0.222
Kurtosis Kurtosis kurtosis	-0.336
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1596000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.997

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ygsa_
Class class	b — All beta proteins
Fold Fold fold	b.26 — SMAD/FHA domain
Superfamily Superfamily superfamily	b.26.1 — SMAD/FHA domain
Family Family family	b.26.1.1 — SMAD domain

CATH v4.4 (1 domains)

Domain ID domain_id	1ygsA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	197.842 Å
Unit-cell length b length_b	197.842 Å
Unit-cell length c length_c	197.842 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	96

Space group space_group	F 41 3 2
Space-group number int_tables_number	210
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2790

Description description	SMAD4
Molecular weight formula_weight	25511.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1658

CRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN

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

SMAD4

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

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

fit	/app/data/saxs_computation/yg/1ygs/1ygs.fit
pddf	/app/data/pr_computation/yg/1ygs/1ygs.pr.out
profile	/app/data/saxs_computation/yg/1ygs/1ygs.dat