SAXSdb — 5mez

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

MH1 domain of human 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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 10–140 Chain B； UniProt 10–140	Not recorded	;DNA (5'-D(PGPCPAPGPGPCPTPAPGPCPCPTPGPCP*A)-3') ; × 2 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

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 5MEZ	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 oligomeric state 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 oligomeric state 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	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 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 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
5MF0 Crystal structure of Smad4-MH1 bound to the GGCCG site. Deposited 2016-11-16	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 5–135； UniProt 10–140 Author chain B； PDBConstruct 5–135； UniProt 10–140

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	5mez
Deposition date deposition_date	2016-11-16
Structure title title	Crystal structure of Smad4-MH1 bound to the GGCT site.
Keywords keywords	Smads, transcription factor, DNA complex, 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	24.25 Å
Radius of gyration Rg (electron density) rg_electron	22.98 Å
Forward intensity I(0) i0	32651700.00
Molecular weight molecular_weight	36544.0 kDa
Excluded volume excluded_volume	42548 Å³
Envelope volume envelope_volume	56696 Å³
Hydration-shell volume shell_volume	21463 Å³
Envelope diameter envelope_diameter	77.0 Å
Shell Rg shell_rg	29.10 Å
Envelope Rg envelope_rg	22.90 Å
Shape Rg shape_rg	22.94 Å
Total Rg total_rg	23.75 Å
Total atoms total_atoms	2523
Residues n_residues	277
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	75.2 Å
Rg (real space) rg_real	24.22 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.2650e+07
I(0) uncertainty (real space) i0_real_error	4.0770e+05
Rg (reciprocal space) rg_reciprocal	24.23 Å
I(0) (reciprocal space) i0_reciprocal	32650000.0000
Solution quality estimate total_estimate	0.9131
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.228
Kurtosis Kurtosis kurtosis	-0.607
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2769000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.970

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MH1 domain of human Smad4
Molecular weight formula_weight	15237.6 kDa
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	2530

GAMGPTSNDACLSIVHSLMCHRQGGESETFAKRAIESLVKKLKEKKDELDSLITAITTNGAHPSKCVTIQRTLDGRLQVAGRKGFPHVIYARLWRWPDLHKNELKHVKYCQYAFDLKCDSVCVNPYHYERVVSPG

来源 Source

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

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PGPCPAPGPGPCPTPAPGPCPCPTPGPCP*A)-3') ;
Molecular weight formula_weight	4899.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D,E

TGCAGGCTAGCCTGCA

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5mezA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	520 — Smad3; Chain A
Homologous superfamily homologous superfamily	10 — SMAD MH1 domain

Domain ID domain_id	5mezB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	520 — Smad3; Chain A
Homologous superfamily homologous superfamily	10 — SMAD MH1 domain

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8. Citations (1)

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Unit-cell length a length_a	64.790 Å
Unit-cell length b length_b	79.060 Å
Unit-cell length c length_c	114.160 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	2.980 Å
Low-resolution limit resolution_low	29.050 Å
R factor r_factor	0.2180
R_work r_work	0.2170
R_free r_free	0.2520

fit	/app/data/saxs_computation/me/5mez/5mez.fit
pddf	/app/data/pr_computation/me/5mez/5mez.pr.out
profile	/app/data/saxs_computation/me/5mez/5mez.dat

Crystal structure of Smad4-MH1 bound to the GGCT site.

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

MH1 domain of human 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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)