SAXSdb — 1g88

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

SMAD4

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 285–552 Chain B； UniProt 285–552 Chain C； UniProt 285–552	Fragment：SMAD4 ACTIVE FRAGMENT Mutation：R515S	No other associated polymer	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

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 1G88	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 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 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
1MR1 Crystal Structure of a Smad4-Ski Complex Deposited 2002-09-17	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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
1YGS CRYSTAL STRUCTURE OF THE SMAD4 TUMOR SUPPRESSOR C-TERMINAL DOMAIN Deposited 1997-10-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 319–552（234 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 319 - 552	Not recorded	No recorded non-water small molecule	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
5C4V Ski-like protein Deposited 2015-06-18	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 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）	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	SMAD4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–268； UniProt 285–552 Author chain B； PDBConstruct 1–268； UniProt 285–552 Author chain C； PDBConstruct 1–268； UniProt 285–552

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	1g88
Deposition date deposition_date	2000-11-16
Structure title title	S4AFL3ARG515 MUTANT
Keywords keywords	transcriptional factor, L3 loop mutant, TRANSCRIPTION; TRANSCRIPTION
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	27.97 Å
Radius of gyration Rg (electron density) rg_electron	26.95 Å
Forward intensity I(0) i0	100946000.00
Molecular weight molecular_weight	77208.0 kDa
Excluded volume excluded_volume	95926 Å³
Envelope volume envelope_volume	119470 Å³
Hydration-shell volume shell_volume	35835 Å³
Envelope diameter envelope_diameter	94.0 Å
Shell Rg shell_rg	35.17 Å
Envelope Rg envelope_rg	27.38 Å
Shape Rg shape_rg	26.95 Å
Total Rg total_rg	27.77 Å
Total atoms total_atoms	5431
Residues n_residues	699
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	88.9 Å
Rg (real space) rg_real	27.85 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	1.0090e+08
I(0) uncertainty (real space) i0_real_error	1.5620e+06
Rg (reciprocal space) rg_reciprocal	27.89 Å
I(0) (reciprocal space) i0_reciprocal	100900000.0000
Solution quality estimate total_estimate	0.9013
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.8 Å
Skewness Skewness skewness	0.218
Kurtosis Kurtosis kurtosis	-0.446
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22790000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1g88a_
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

Domain ID domain_id	d1g88b_
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

Domain ID domain_id	d1g88c_
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 (3 domains)

Domain ID domain_id	1g88A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1g88B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1g88C00
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	140.855 Å
Unit-cell length b length_b	140.855 Å
Unit-cell length c length_c	194.613 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	48

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	40.500 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2634

Description description	SMAD4
Molecular weight formula_weight	29348.3 kDa
Mutation mutation	R515S
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5431

S4AFL3ARG515 MUTANT

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/g8/1g88/1g88.fit
pddf	/app/data/pr_computation/g8/1g88/1g88.pr.out
profile	/app/data/saxs_computation/g8/1g88/1g88.dat