SAXSdb — 6duy

▼

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

Catenin alpha-2

Mus musculus

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 664–918 Chain B； UniProt 664–918	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；277 K；100 mM sodium acetate/acetic acid, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic	Resolution 2.81 Å R-free 0.255

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 6DUY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4K1O Crystal structure of the alphaN-catenin actin-binding domain Deposited 2013-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 651–905（255 aa） Fragment：C-terminal actin-binding domain	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；0.1M HEPES, pH 7.0, 1.6 M (NH4)2SO4, 0.2 M NaCl,and 0.1M K/Na tartate, vapor diffusion, temperature 277K	Resolution 2.60 Å R-free 0.231
4K1O Crystal structure of the alphaN-catenin actin-binding domain Deposited 2013-04-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 651–905（255 aa） Fragment：C-terminal actin-binding domain	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；0.1M HEPES, pH 7.0, 1.6 M (NH4)2SO4, 0.2 M NaCl,and 0.1M K/Na tartate, vapor diffusion, temperature 277K	Resolution 2.60 Å R-free 0.231
4ONS Structural and thermodynamic characterization of cadherin-beta-catenin-alpha-catenin complex formation Deposited 2014-01-29	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 A 18–264（247 aa） Fragment：beta-catenin binding domain, UNP residues 18-264	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；283 K；100mM Tris-Cl, 22% polyethylene glycol monomethryl ether, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.80 Å R-free 0.264
4ONS Structural and thermodynamic characterization of cadherin-beta-catenin-alpha-catenin complex formation Deposited 2014-01-29	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 C 18–264（247 aa） Fragment：beta-catenin binding domain, UNP residues 18-264	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；283 K；100mM Tris-Cl, 22% polyethylene glycol monomethryl ether, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.80 Å R-free 0.264
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 13–261（249 aa） Fragment：UNP residues 13-261	Not recorded	IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide	Resolution 2.50 Å R-free 0.234
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 13–261（249 aa） Fragment：UNP residues 13-261	Not recorded	IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide	Resolution 2.50 Å R-free 0.234
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 13–261（249 aa） Fragment：UNP residues 13-261	Not recorded	IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide	Resolution 2.50 Å R-free 0.234
4P9T Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin Deposited 2014-04-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 13–261（249 aa） Fragment：UNP residues 13-261	Not recorded	IOD IODIDE ION × 5 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, 0.1 M Bis-Tris propane (pH 6.5), 0.2 M Sodium iodide	Resolution 2.50 Å R-free 0.234
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 260–632（373 aa） Fragment：UNP residues 260-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K	Resolution 2.45 Å R-free 0.267
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 260–632（373 aa） Fragment：UNP residues 260-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K	Resolution 2.45 Å R-free 0.267
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 260–632（373 aa） Fragment：UNP residues 260-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K	Resolution 2.45 Å R-free 0.267
5XFL Crystal structure of the force-sensing device region of alpha N-catenin Deposited 2017-04-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 260–632（373 aa） Fragment：UNP residues 260-632	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；100MM HEPES, 20% PEG3350, 200MM POTASSIUM FORMATE, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K	Resolution 2.45 Å R-free 0.267

4 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CTNA2_MOUSE
Isoform	Q61301-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–257； UniProt 664–918 Author chain B； PDBConstruct 3–257； UniProt 664–918

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6duy
Deposition date deposition_date	2018-06-22
Structure title title	Crystal structure of the alpha-N-catenin actin-binding domain H1 mutant
Keywords keywords	five-helix bundle, F-actin-binding, mechanosensor, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.32 Å
Radius of gyration Rg (electron density) rg_electron	23.42 Å
Forward intensity I(0) i0	29501300.00
Molecular weight molecular_weight	41367.0 kDa
Excluded volume excluded_volume	51839 Å³
Envelope volume envelope_volume	66555 Å³
Hydration-shell volume shell_volume	24040 Å³
Envelope diameter envelope_diameter	83.7 Å
Shell Rg shell_rg	29.86 Å
Envelope Rg envelope_rg	24.10 Å
Shape Rg shape_rg	23.46 Å
Total Rg total_rg	24.11 Å
Total atoms total_atoms	2884
Residues n_residues	381
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.4 Å
Rg (real space) rg_real	24.26 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	2.9500e+07
I(0) uncertainty (real space) i0_real_error	4.1260e+05
Rg (reciprocal space) rg_reciprocal	24.28 Å
I(0) (reciprocal space) i0_reciprocal	29500000.0000
Solution quality estimate total_estimate	0.8814
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	0.256
Kurtosis Kurtosis kurtosis	-0.342
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	7733000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.981

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6duyA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

Domain ID domain_id	6duyB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	230 — Alpha-catenin/vinculin-like

▶

8. Citations (1)

▶

Unit-cell length a length_a	75.094 Å
Unit-cell length b length_b	82.845 Å
Unit-cell length c length_c	105.309 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	orthorhombic

Resolution resolution	2.810 Å
Low-resolution limit resolution_low	44.440 Å
R factor r_factor	0.2042
R_work r_work	0.1986
R_free r_free	0.2548

Description description	Catenin alpha-2
Molecular weight formula_weight	28120.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2916

Crystal structure of the alpha-N-catenin actin-binding domain H1 mutant

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

Catenin alpha-2

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

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

fit	/app/data/saxs_computation/du/6duy/6duy.fit
pddf	/app/data/pr_computation/du/6duy/6duy.pr.out
profile	/app/data/saxs_computation/du/6duy/6duy.dat