SAXSdb — 4r7x

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

Arrestin domain-containing protein 3

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–180	Fragment：UNP residues 1-180	PO4 PHOSPHATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.75M NH4H2PO4, 0.1M Sodium citrate tribasic dehydrate, 3.0% (W/V) 6-Aminohexanoic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.61 Å R-free 0.252
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–180	Fragment：UNP residues 1-180	PO4 PHOSPHATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.75M NH4H2PO4, 0.1M Sodium citrate tribasic dehydrate, 3.0% (W/V) 6-Aminohexanoic acid, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.61 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 4R7X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4N7H Crystal Structure of the Complex of 3rd WW domain of Human Nedd4 and 1st PPXY Motif of ARRDC3 Deposited 2013-10-15	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 B 342–354（13 aa） Fragment：1st PPXY Motif (UNP residues 342-354)	Not recorded	GAI GUANIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；0.35M (NH4)SO4, 100mM Tris-HCl 8.0, 100mM Guanidine-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.70 Å R-free 0.233
4R7V Crystal structure of N-lobe of human ARRDC3(1-165) Deposited 2014-08-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–165（165 aa） Fragment：UNP residues 1-165	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；20% PEG 3350, 0.1M Tris-HCl, 0.2M (NH4)2SO4, 50mM Guanidine-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.73 Å R-free 0.221

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARRD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–185； UniProt 1–180 Author chain B； PDBConstruct 6–185； UniProt 1–180

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	4r7x
Deposition date deposition_date	2014-08-28
Structure title title	Crystal structure of N-lobe of human ARRDC3(1-180)
Keywords keywords	arrestin fold, GPCR downregulation, Beat 2 adrenergic receptor, PROTEIN BINDING; PROTEIN BINDING
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	21.63 Å
Radius of gyration Rg (electron density) rg_electron	20.82 Å
Forward intensity I(0) i0	23364800.00
Molecular weight molecular_weight	35123.0 kDa
Excluded volume excluded_volume	43300 Å³
Envelope volume envelope_volume	55408 Å³
Hydration-shell volume shell_volume	22149 Å³
Envelope diameter envelope_diameter	78.4 Å
Shell Rg shell_rg	27.57 Å
Envelope Rg envelope_rg	21.38 Å
Shape Rg shape_rg	20.83 Å
Total Rg total_rg	21.68 Å
Total atoms total_atoms	2472
Residues n_residues	299
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	74.2 Å
Rg (real space) rg_real	21.57 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	2.3360e+07
I(0) uncertainty (real space) i0_real_error	3.2460e+05
Rg (reciprocal space) rg_reciprocal	21.58 Å
I(0) (reciprocal space) i0_reciprocal	23360000.0000
Solution quality estimate total_estimate	0.7932
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.286
Kurtosis Kurtosis kurtosis	-0.322
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4229000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

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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	Arrestin domain-containing protein 3
Molecular weight formula_weight	20891.3 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	2485

GAMGSMVLGKVKSLTISFDCLNDSNVPVYSSGDTVSGRVNLEVTGEIRVKSLKIHARGHAKVRWTESRNAGSNTAYTQNYTEEVEYFNHKDILIGHERDDDNSEEGFHTIHSGRHEYAFSFELPQTPLATSFEGRHGSVRYWVKAELHRPWLLPVKLKKEFTVFEHIDINTPSLLSPQAGTKEKT

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 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	13

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4r7xA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

Domain ID domain_id	4r7xB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

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8. Citations (1)

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Unit-cell length a length_a	107.941 Å
Unit-cell length b length_b	107.941 Å
Unit-cell length c length_c	117.778 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.610 Å
Low-resolution limit resolution_low	32.026 Å
R factor r_factor	0.2104
R_work r_work	0.2082
R_free r_free	0.2518

fit	/app/data/saxs_computation/r7/4r7x/4r7x.fit
pddf	/app/data/pr_computation/r7/4r7x/4r7x.pr.out
profile	/app/data/saxs_computation/r7/4r7x/4r7x.dat

Crystal structure of N-lobe of human ARRDC3(1-180)

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

Arrestin domain-containing protein 3

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