SAXSdb — 2vmb

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

GENERAL SECRETION PATHWAY PROTEIN F

VIBRIO CHOLERAE

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 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GSPF_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–116； UniProt 56–170 Author chain B； PDBConstruct 2–116； UniProt 56–170

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	2vmb
Deposition date deposition_date	2008-01-25
Structure title title	The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae
Keywords keywords	;TRANSMEMBRANE, INNER MEMBRANE, TYPE 2 SECRETION, T4PB, T2SS, VIBRIO, CHOLERA, MEMBRANE, TRANSPORT, PROTEIN SECRETION, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
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.

2vmb__assembly_1__model_1

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

Download this curve (.dat)

2vmb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vmb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.45 Å
Rg (electron density)	15.50 Å
Total Rg	16.39 Å
Atom count	952
Residues	121
Excluded volume	16977 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vmb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vmb__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)

Entity 1 Entity 1 polymer

Description description	GENERAL SECRETION PATHWAY PROTEIN F
Molecular weight formula_weight	13843.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2104

MGFAFKRGISTPDLALITRQLATLVQSGMPLEECLRAVAEQSEKPRIRTMLVAVRAKVTEGYTLSDSLGDYPHVFDELFRSMVAAGEKSGHLDSVLERLADYAENRQKMRSKLQQASENLYFQ

Source Source

Source organism organism	VIBRIO CHOLERAE
NCBI taxonomy ID ncbi_taxonomy_id	666
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	207

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vmbA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	81 — Receptor-associated Protein
Homologous superfamily homologous superfamily	30 — Type II secretion system (T2SS), domain F

Domain ID domain_id	2vmbB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	81 — Receptor-associated Protein
Homologous superfamily homologous superfamily	30 — Type II secretion system (T2SS), domain F

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Unit-cell length a length_a	49.197 Å
Unit-cell length b length_b	53.832 Å
Unit-cell length c length_c	89.070 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	46.080 Å
R factor r_factor	0.1920
R_work r_work	0.1890
R_free r_free	0.2510

The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae

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

GENERAL SECRETION PATHWAY PROTEIN F

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

2vmb__assembly_1__model_1

2vmb__assembly_1__model_1 | I(q)

2vmb__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae

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

GENERAL SECRETION PATHWAY PROTEIN F

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

2vmb__assembly_1__model_1

2vmb__assembly_1__model_1 | I(q)

2vmb__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

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)