SAXSdb — 3gn9

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

Type II secretory pathway, pseudopilin EpsG

Vibrio vulnificus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 D-MALATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 D-MALATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8DDT3_VIBVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–115； UniProt 36–147 Author chain B； PDBConstruct 4–115； UniProt 36–147 Author chain C； PDBConstruct 4–115； UniProt 36–147

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	3gn9
Deposition date deposition_date	2009-03-16
Structure title title	Crystal structure of the major pseudopilin from the type 2 secretion system of Vibrio vulnificus
Keywords keywords	GENERAL SECRETORY PATHWAY, MAJOR PILIN, PROTEIN TRANSPORT, COMPLEX, Methylation; PROTEIN TRANSPORT
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.

3gn9__assembly_1__model_1

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

Download this curve (.dat)

3gn9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gn9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.59 Å
Rg (electron density)	14.35 Å
Total Rg	15.46 Å
Atom count	877
Residues	112
Excluded volume	15330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gn9__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gn9__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gn9__assembly_3__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 (4)

Entity 1 Entity 1 polymer

Description description	Type II secretory pathway, pseudopilin EpsG
Molecular weight formula_weight	12585.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2930

GAMGNKEKADQQKAITDIVALENALDMYKLDNSVYPTTDQGLEALVTKPSSPEPRNYRNGGYIKRLPKDPWGNEYQYMSPGDKGTIDIFTLGADGQEGGEGAAADIGNWNMQDFQ

Source Source

Source organism organism	Vibrio vulnificus
NCBI taxonomy ID ncbi_taxonomy_id	672
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	D-MALATE
Molecular weight formula_weight	134.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	266

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3gn9A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	700 — Glycoprotein, Type 4 Pilin
Homologous superfamily homologous superfamily	10 — Glycoprotein, Type 4 Pilin

Domain ID domain_id	3gn9B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	700 — Glycoprotein, Type 4 Pilin
Homologous superfamily homologous superfamily	10 — Glycoprotein, Type 4 Pilin

Domain ID domain_id	3gn9C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	700 — Glycoprotein, Type 4 Pilin
Homologous superfamily homologous superfamily	10 — Glycoprotein, Type 4 Pilin

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Unit-cell length a length_a	100.180 Å
Unit-cell length b length_b	104.510 Å
Unit-cell length c length_c	55.410 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.860 Å
Low-resolution limit resolution_low	38.900 Å
R factor r_factor	0.1790
R_work r_work	0.1780
R_free r_free	0.2040

Crystal structure of the major pseudopilin from the type 2 secretion system of Vibrio vulnificus

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

Type II secretory pathway, pseudopilin EpsG

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

3gn9__assembly_1__model_1

3gn9__assembly_1__model_1 | I(q)

3gn9__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of the major pseudopilin from the type 2 secretion system of Vibrio vulnificus

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

Type II secretory pathway, pseudopilin EpsG

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

3gn9__assembly_1__model_1

3gn9__assembly_1__model_1 | I(q)

3gn9__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)