SAXSdb — 5suy

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

Segment polarity protein dishevelled homolog DVL-2

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 416–510 Chain B； UniProt 416–510 Chain C； UniProt 416–510 Chain D； UniProt 416–510	Fragment：UNP residues 416-510	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M MES 0.1 M NaCl 0.1 M Li2SO4 22-26% PEG400	Resolution 1.88 Å R-free 0.217

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 5SUY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2REY Crystal structure of the PDZ domain of human dishevelled 2 (homologous to Drosophila dsh) Deposited 2007-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 260–354（95 aa） Fragment：PDZ domain: Residues 261-355	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2M Ammonium acetate, 0.1M Bis-tris pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.55 Å R-free 0.240
3CBX The Dvl2 PDZ Domain in Complex with the C1 Inhibitory Peptide Deposited 2008-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354) Chain B 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354)	Mutation：C341S Mutation：C341S	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；292 K；60% 2-Methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.70 Å R-free 0.227
3CBY The Dvl2 PDZ Domain in Complex with the N1 Inhibitory Peptide Deposited 2008-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354) Chain B 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354)	Mutation：C341S Mutation：C341S	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；1.6 M tri-sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.50 Å R-free 0.182
3CBZ The Dvl2 PDZ Domain in Complex with the N2 Inhibitory Peptide Deposited 2008-02-23	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 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354)	Mutation：C341S	PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；0.1 M HEPES, 0.8 M sodium phosphate, 0.8 M Potassium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.38 Å R-free 0.166
3CC0 The Dvl2 PDZ Domain in Complex with the N3 Inhibitory Peptide Deposited 2008-02-23	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 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354) Chain B 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354) Chain C 264–354（91 aa） Fragment：PDZ domain (UNP residues 264-354)	Mutation：C341S Mutation：C341S Mutation：C341S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；292 K；1.0 M Ammonium citrate tribasic, 0.1 M BIS-TRIS propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.75 Å R-free 0.238
4WIP DIX domain of human Dvl2 Deposited 2014-09-26	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 12–106（95 aa） Fragment：UNP residues 13-105 Chain B 12–106（95 aa） Fragment：UNP residues 13-105 Chain C 12–106（95 aa） Fragment：UNP residues 13-105	Mutation：Y27D Mutation：Y27D Mutation：Y27D	1PE PENTAETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；grew in PEG400 (cryo condition) over night	Resolution 2.69 Å R-free 0.248
5LNP Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from monomeric fraction Deposited 2016-08-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 416–510（95 aa） Fragment：DEP domain, UNP residues 416-510 Chain B 416–510（95 aa） Fragment：DEP domain, UNP residues 416-510 Chain C 416–510（95 aa） Fragment：DEP domain, UNP residues 416-510 Chain D 416–510（95 aa） Fragment：DEP domain, UNP residues 416-510	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M MES, pH=6.5 0.1 M NaCl 0.1 M Li2SO4 23 % PEG400	Resolution 1.99 Å R-free 0.246
5SUZ Domain-swapped dimer of human Dishevelled2 DEP domain: C-centered monoclinic crystal form crystallised from monomeric fraction Deposited 2016-08-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 416–509（94 aa） Fragment：UNP residues 416-509 Chain B 416–509（94 aa） Fragment：UNP residues 416-509	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, pH=6.5 0.2 M CaCl2 23% PEG350 MME	Resolution 1.84 Å R-free 0.263
6IW3 High resolution structure of Dvl2-DIX Y27W/C80S mutant Deposited 2018-12-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 12–93（82 aa） Fragment：DIX-domain	Mutation：Y27W, C80S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；20% (w/v) PEG 6000, Tris-HCl pH 8.0, 200 mM lithium chloride	Resolution 1.64 Å R-free 0.229
6JCK Complex structure of Axin-DIX and Dvl2-DIX Deposited 2019-01-29	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 B 12–93（82 aa）	Mutation：V67A,K68A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；25% (w/v) PEG1500, 0.1 M Malonate-Imidazole-Borate buffer pH 7.0	Resolution 3.09 Å R-free 0.290
8WM9 Fzd4/DEP complex Deposited 2023-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–736（736 aa）	Not recorded	Y01 CHOLESTEROL HEMISUCCINATE × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.53 Å
8WMA Fzd4/DEP complex (local refined) Deposited 2023-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–736（736 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.47 Å
8WWR Crystal structure of apo human dishevelled 2 (Dvl2) PDZ domain Deposited 2023-10-26	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 261–354（94 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Tri-sodium citrate, pH 5.6 20% (v/v) Isopropanol 20%(w/v) PEG4000	Resolution 1.75 Å R-free 0.253
8YR7 Crystal structure of human dishevelled 2 (Dvl2) PDZ domain fused with WGEF internal peptide motif Deposited 2024-03-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 261–353（93 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.1M Sodium acetate (pH 4.5), 3M Sodium chloride	Resolution 3.00 Å R-free 0.335

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DVL2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–97； UniProt 416–510 Author chain B； PDBConstruct 3–97； UniProt 416–510 Author chain C； PDBConstruct 3–97； UniProt 416–510 Author chain D； PDBConstruct 3–97； UniProt 416–510

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	5suy
Deposition date deposition_date	2016-08-04
Structure title title	Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from dimeric fraction
Keywords keywords	Dishevelled, DEP domain, WNT signalling, signaling protein; SIGNALING 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	25.60 Å
Radius of gyration Rg (electron density) rg_electron	24.67 Å
Forward intensity I(0) i0	31317300.00
Molecular weight molecular_weight	42795.0 kDa
Excluded volume excluded_volume	53542 Å³
Envelope volume envelope_volume	71075 Å³
Hydration-shell volume shell_volume	24879 Å³
Envelope diameter envelope_diameter	82.2 Å
Shell Rg shell_rg	30.96 Å
Envelope Rg envelope_rg	24.37 Å
Shape Rg shape_rg	24.68 Å
Total Rg total_rg	25.45 Å
Total atoms total_atoms	3011
Residues n_residues	378
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	80.6 Å
Rg (real space) rg_real	25.52 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	3.1320e+07
I(0) uncertainty (real space) i0_real_error	4.4530e+05
Rg (reciprocal space) rg_reciprocal	25.55 Å
I(0) (reciprocal space) i0_reciprocal	31320000.0000
Solution quality estimate total_estimate	0.9040
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	35.1 Å
Skewness Skewness skewness	0.168
Kurtosis Kurtosis kurtosis	-0.554
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14400000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.944

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Segment polarity protein dishevelled homolog DVL-2
Molecular weight formula_weight	10846.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	3147

SSGLSVHTDMASVTKAMAAPESGLEVRDRMWLKITIPNAFLGSDVVDWLYHHVEGFPERREARKYASGLLKAGLIRHTVNKITFSEQCYYVFGDLSG

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	117

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d5suya1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.31 — DEP domain

Domain ID domain_id	d5suya2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5suyb1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.31 — DEP domain

Domain ID domain_id	d5suyb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5suyc1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.31 — DEP domain

Domain ID domain_id	d5suyc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5suyd_
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.5 — 'Winged helix' DNA-binding domain
Family Family family	a.4.5.31 — DEP domain

CATH v4.4 (4 domains)

Domain ID domain_id	5suyA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5suyB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5suyC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5suyD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	61.671 Å
Unit-cell length b length_b	60.174 Å
Unit-cell length c length_c	66.128 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	41.980 Å
R factor r_factor	0.1864
R_work r_work	0.1847
R_free r_free	0.2170

fit	/app/data/saxs_computation/su/5suy/5suy.fit
pddf	/app/data/pr_computation/su/5suy/5suy.pr.out
profile	/app/data/saxs_computation/su/5suy/5suy.dat

Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from dimeric fraction

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

Segment polarity protein dishevelled homolog DVL-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