SAXSdb — 6nyj

▼

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

Vacuolating cytotoxin autotransporter

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VACA2_HELPX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–821； UniProt 34–854 Author chain B； PDBConstruct 1–821； UniProt 34–854 Author chain C； PDBConstruct 1–821； UniProt 34–854 Author chain D； PDBConstruct 1–821； UniProt 34–854 Author chain E； PDBConstruct 1–821； UniProt 34–854 Author chain F； PDBConstruct 1–821； UniProt 34–854 Author chain G； PDBConstruct 1–821； UniProt 34–854 Author chain H； PDBConstruct 1–821； UniProt 34–854 Author chain I； PDBConstruct 1–821； UniProt 34–854 Author chain J； PDBConstruct 1–821； UniProt 34–854 Author chain K； PDBConstruct 1–821； UniProt 34–854 Author chain L； PDBConstruct 1–821； UniProt 34–854

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nyj
Deposition date deposition_date	2019-02-11
Structure title title	Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2b (OA-2b)
Keywords keywords	Helicobacter pylori, vacuolating cytotoxin A, pore-forming toxin, TOXIN; TOXIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

6nyj__assembly_1__model_1

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

Download this curve (.dat)

6nyj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6nyj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	90.98 Å
Rg (electron density)	90.78 Å
Total Rg	90.98 Å
Atom count	68664
Residues	9000
Excluded volume	1211900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6nyj__assembly_1__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (1)

▶

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	—

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

Resolution resolution	3.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	47009

Description description	Vacuolating cytotoxin autotransporter
Molecular weight formula_weight	88463.2 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	68664

Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2b (OA-2b)

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

Vacuolating cytotoxin autotransporter

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

6nyj__assembly_1__model_1

6nyj__assembly_1__model_1 | I(q)

6nyj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Citations (1)

Helicobacter pylori Vacuolating Cytotoxin A Oligomeric Assembly 2b (OA-2b)

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

Vacuolating cytotoxin autotransporter

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

6nyj__assembly_1__model_1

6nyj__assembly_1__model_1 | I(q)

6nyj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Citations (1)