SAXSdb — 1vgf

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

volvatoxin A2

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ACETATE ION × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACETATE ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6USC4_9AGAR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–199； UniProt 19–217 Author chain B； PDBConstruct 1–199； UniProt 19–217

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	1vgf
Deposition date deposition_date	2004-04-24
Structure title title	volvatoxin A2 (diamond crystal form)
Keywords keywords	toxin, pore formation, fungus, cardiotoxin; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1vgf__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vgf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vgf__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.30 Å
Rg (electron density)	17.01 Å
Total Rg	18.08 Å
Atom count	1559
Residues	194
Excluded volume	27913 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vgf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vgf__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1vgfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.103 — CytB endotoxin-like
Superfamily Superfamily superfamily	d.103.1 — CytB endotoxin-like
Family Family family	d.103.1.1 — CytB endotoxin-like

Domain ID domain_id	d1vgfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.103 — CytB endotoxin-like
Superfamily Superfamily superfamily	d.103.1 — CytB endotoxin-like
Family Family family	d.103.1.1 — CytB endotoxin-like

CATH v4.4 (2 domains)

Domain ID domain_id	1vgfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	198 — Delta-endotoxin CytB
Homologous superfamily homologous superfamily	10 — Delta-endotoxin CytB-like

Domain ID domain_id	1vgfB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	198 — Delta-endotoxin CytB
Homologous superfamily homologous superfamily	10 — Delta-endotoxin CytB-like

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Unit-cell length a length_a	56.310 Å
Unit-cell length b length_b	56.310 Å
Unit-cell length c length_c	264.919 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 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	28.540 Å
R factor r_factor	—
R_work r_work	0.2140
R_free r_free	0.2680

Description description	volvatoxin A2
Molecular weight formula_weight	22357.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3156

volvatoxin A2 (diamond crystal form)

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

volvatoxin A2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1vgf__assembly_1__model_1

1vgf__assembly_1__model_1 | I(q)

1vgf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	7

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

volvatoxin A2 (diamond crystal form)

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

volvatoxin A2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1vgf__assembly_1__model_1

1vgf__assembly_1__model_1 | I(q)

1vgf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)