SAXSdb — 1oma

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

OMEGA-AGA-IVB

Agelenopsis aperta

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 36–83	Not recorded	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	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 1OMA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AGG THE SOLUTION STRUCTURE OF OMEGA-AGA-IVB, A P-TYPE CALCIUM CHANNEL ANTAGONIST FROM THE VENOM OF AGELENOPSIS APERTA Deposited 1995-11-03	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–83（48 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1OMB SEQUENTIAL ASSIGNMENT AND STRUCTURE DETERMINATION OF SPIDER TOXIN OMEGA-AGA-IVB Deposited 1993-09-09	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–83（48 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided

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

View Construct and Data Evidence

UniProt name	TOG4B_AGEAP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–48； UniProt 36–83

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	1oma
Deposition date deposition_date	1993-09-09
Structure title title	SEQUENTIAL ASSIGNMENT AND STRUCTURE DETERMINATION OF SPIDER TOXIN OMEGA-AGA-IVB
Keywords keywords	TOXIN; TOXIN
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	11.73 Å
Radius of gyration Rg (electron density) rg_electron	12.09 Å
Forward intensity I(0) i0	230339000.00
Molecular weight molecular_weight	110900.0 kDa
Excluded volume excluded_volume	132520 Å³
Envelope volume envelope_volume	33179 Å³
Hydration-shell volume shell_volume	16274 Å³
Envelope diameter envelope_diameter	57.0 Å
Shell Rg shell_rg	23.40 Å
Envelope Rg envelope_rg	17.91 Å
Shape Rg shape_rg	12.15 Å
Total Rg total_rg	12.41 Å
Total atoms total_atoms	14637
Residues n_residues	1008
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	51.4 Å
Rg (real space) rg_real	11.89 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	2.3030e+08
I(0) uncertainty (real space) i0_real_error	2.8380e+06
Rg (reciprocal space) rg_reciprocal	11.89 Å
I(0) (reciprocal space) i0_reciprocal	230300000.0000
Solution quality estimate total_estimate	0.6886
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	11.7 Å
Skewness Skewness skewness	0.683
Kurtosis Kurtosis kurtosis	0.362
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	111900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.289; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.082; Smooth: 1.000

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1omaa_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.6 — omega toxin-like
Family Family family	g.3.6.2 — Spider toxins

CATH v4.4 (1 domains)

Domain ID domain_id	1omaA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	40 — Omega-AgatoxinV
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	OMEGA-AGA-IVB
Molecular weight formula_weight	5287.1 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	14637

来源生物 organism	Agelenopsis aperta
NCBI Class编号 ncbi_taxonomy_id	6908

SEQUENTIAL ASSIGNMENT AND STRUCTURE DETERMINATION OF SPIDER TOXIN OMEGA-AGA-IVB

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

OMEGA-AGA-IVB

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/om/1oma/1oma.fit
pddf	/app/data/pr_computation/om/1oma/1oma.pr.out
profile	/app/data/saxs_computation/om/1oma/1oma.dat