SAXSdb — 3cw3

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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 1022–1117	Fragment：non-lens vertebrate beta-gamma-crystallin domain	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

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 3CW3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DAD Solution structure of the fifth crystall domain of the non-lens protein, Absent in melanoma 1 Deposited 2005-12-13	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 1416–1495（80 aa） Fragment：The fifth crystall domain	Not recorded	No recorded non-water small molecule	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
6VRO The structure of the PP2A B56 subunit AIM1 complex Deposited 2020-02-08	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 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 1–96； UniProt 1022–1117

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	3cw3
Deposition date deposition_date	2008-04-21
Structure title title	Crystal structure of AIM1g1
Keywords keywords	beta gamma-crystallin; greek key; tryptophan corner;, Lectin, ONCOPROTEIN; ONCOPROTEIN
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	14.76 Å
Radius of gyration Rg (electron density) rg_electron	13.27 Å
Forward intensity I(0) i0	2291580.00
Molecular weight molecular_weight	10587.0 kDa
Excluded volume excluded_volume	13341 Å³
Envelope volume envelope_volume	15464 Å³
Hydration-shell volume shell_volume	10263 Å³
Envelope diameter envelope_diameter	45.4 Å
Shell Rg shell_rg	18.52 Å
Envelope Rg envelope_rg	13.67 Å
Shape Rg shape_rg	13.25 Å
Total Rg total_rg	14.56 Å
Total atoms total_atoms	746
Residues n_residues	93
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	47.6 Å
Rg (real space) rg_real	14.68 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.2920e+06
I(0) uncertainty (real space) i0_real_error	2.4940e+04
Rg (reciprocal space) rg_reciprocal	14.69 Å
I(0) (reciprocal space) i0_reciprocal	2292000.0000
Solution quality estimate total_estimate	0.8938
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.3 Å
Skewness Skewness skewness	0.143
Kurtosis Kurtosis kurtosis	-0.367
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	279000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

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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	Absent in melanoma 1 protein
Molecular weight formula_weight	10817.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	856

GKVVIYSEPDVSEKCIEVFSDIQDCSSWSLSPVILIKVVRGCWILYEQPNFEGHSIPLEEGELELSGLWGIEDILERHEEAESDKPVVIGSIRHVV

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	110

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3cw3A00
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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Unit-cell length a length_a	54.964 Å
Unit-cell length b length_b	54.964 Å
Unit-cell length c length_c	59.574 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1810
R_free r_free	0.2320

fit	/app/data/saxs_computation/cw/3cw3/3cw3.fit
pddf	/app/data/pr_computation/cw/3cw3/3cw3.pr.out
profile	/app/data/saxs_computation/cw/3cw3/3cw3.dat

Crystal structure of AIM1g1

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction