SAXSdb — 2dad

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

Absent in melanoma 1 protein

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 1416–1495	Fragment：The fifth crystall domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.1mM protein U-15N,13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2DAD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3CW3 Crystal structure of AIM1g1 Deposited 2008-04-21	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1022–1117（96 aa） Fragment：non-lens vertebrate beta-gamma-crystallin domain	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.3-1.5M NaCitrate;0.1M HepesNa 7.5; 3%isopropanol (or)0.4M NaCl, vapor diffusion, hanging drop, temperature 298K	Resolution 1.88 Å R-free 0.232
6VRO The structure of the PP2A B56 subunit AIM1 complex Deposited 2020-02-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 716–741（26 aa） Fragment：UNP residues 716-741	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Tris, pH 8.0, 9% PEG8000, 0.9 M lithium chloride	Resolution 2.45 Å R-free 0.235

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

View Construct and Data Evidence

UniProt name	AIM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–87； UniProt 1416–1495

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	2dad
Deposition date deposition_date	2005-12-13
Structure title title	Solution structure of the fifth crystall domain of the non-lens protein, Absent in melanoma 1
Keywords keywords	;crystall domain, greek key pattern, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, ONCOPROTEIN ;; ONCOPROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.76 Å
Radius of gyration Rg (electron density) rg_electron	12.20 Å
Forward intensity I(0) i0	628614000.00
Molecular weight molecular_weight	197410.0 kDa
Excluded volume excluded_volume	240020 Å³
Envelope volume envelope_volume	23977 Å³
Hydration-shell volume shell_volume	13374 Å³
Envelope diameter envelope_diameter	49.8 Å
Shell Rg shell_rg	21.17 Å
Envelope Rg envelope_rg	16.21 Å
Shape Rg shape_rg	12.18 Å
Total Rg total_rg	12.46 Å
Total atoms total_atoms	26500
Residues n_residues	1860
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	44.9 Å
Rg (real space) rg_real	12.71 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	6.2860e+08
I(0) uncertainty (real space) i0_real_error	7.5010e+06
Rg (reciprocal space) rg_reciprocal	12.71 Å
I(0) (reciprocal space) i0_reciprocal	628600000.0000
Solution quality estimate total_estimate	0.8383
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.0 Å
Skewness Skewness skewness	0.259
Kurtosis Kurtosis kurtosis	-0.053
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	232500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.643; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.981

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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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2dada1
Class class	b — All beta proteins
Fold Fold fold	b.11 — gamma-Crystallin-like
Superfamily Superfamily superfamily	b.11.1 — gamma-Crystallin-like
Family Family family	b.11.1.0 — automated matches

Domain ID domain_id	d2dada2
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	d2dada3
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

CATH v4.4 (1 domains)

Domain ID domain_id	2dadA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	20 — Gamma-B Crystallin; domain 1
Homologous superfamily homologous superfamily	10 — Crystallins

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8. Citations (1)

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Description description	Absent in melanoma 1 protein
Molecular weight formula_weight	9899.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	26500

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/da/2dad/2dad.fit
pddf	/app/data/pr_computation/da/2dad/2dad.pr.out
profile	/app/data/saxs_computation/da/2dad/2dad.dat

Solution structure of the fifth crystall domain of the non-lens protein, Absent in melanoma 1

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

Absent in melanoma 1 protein

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)