SAXSdb — 2vt1

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

SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS

SHIGELLA FLEXNERI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPAS_SHIFL
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 2–52； UniProt 207–257 Author chain B； PDBConstruct 1–85； UniProt 258–342

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	2vt1
Deposition date deposition_date	2008-05-08
Structure title title	Crystal structure of the cytoplasmic domain of Spa40, the specificity switch for the Shigella flexneri Type III Secretion System
Keywords keywords	;SHIGELLA FLEXNERI, SPECIFICITY SWITCH, VIRULENCE, TRANSMEMBRANE, INNER MEMBRANE, FLHB, YSCU, T3SS, SPA40, PLASMID, MEMBRANE, TYPE III SECRETION SYSTEM, MEMBRANE PROTEIN ;; MEMBRANE 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.

2vt1__assembly_1__model_1

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

Download this curve (.dat)

2vt1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vt1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.31 Å
Rg (electron density)	12.99 Å
Total Rg	14.35 Å
Atom count	806
Residues	102
Excluded volume	14588 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vt1__assembly_1__model_1`	dimeric （2）	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	SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS
Molecular weight formula_weight	6394.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	838

MDMMMDKQEIKREYIEQEGHFETKSRRRELHIEILSEQTKSDIRNSKLVVMN

Source Source

Source organism organism	SHIGELLA FLEXNERI
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS
Molecular weight formula_weight	10890.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PTHIAIGIYFNPEIAPAPFISLIETNQCALAVRKYANEVGIPTVRDVKLARKLYKTHTKYSFVDFEHLDEVLRLIVWLEQVENTHLEHHHHHH

Source Source

Source organism organism	SHIGELLA FLEXNERI
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2vt1.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.367 — EscU C-terminal domain-like
Superfamily Superfamily superfamily	d.367.1 — EscU C-terminal domain-like
Family Family family	d.367.1.1 — EscU C-terminal domain-like

CATH v4.4 (1 domains)

Domain ID domain_id	2vt1B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1690 — name from scop
Homologous superfamily homologous superfamily	10 — secretion proteins EscU

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Unit-cell length a length_a	25.035 Å
Unit-cell length b length_b	30.753 Å
Unit-cell length c length_c	32.099 Å
Unit-cell angle α angle_alpha	102.52 °
Unit-cell angle β angle_beta	110.97 °
Unit-cell angle γ angle_gamma	94.30 °
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	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.590 Å
R factor r_factor	0.1800
R_work r_work	0.1780
R_free r_free	0.2270

Crystal structure of the cytoplasmic domain of Spa40, the specificity switch for the Shigella flexneri Type III Secretion System

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

SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS

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

2vt1__assembly_1__model_1

2vt1__assembly_1__model_1 | I(q)

2vt1__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the cytoplasmic domain of Spa40, the specificity switch for the Shigella flexneri Type III Secretion System

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

SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS

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

2vt1__assembly_1__model_1

2vt1__assembly_1__model_1 | I(q)

2vt1__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)