SAXSdb — 1yjg

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

Surface protein VspA

Borrelia turicatae

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
2	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	O34000
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 45–202 Author chain B； PDBConstruct 1–158； UniProt 45–202 Author chain D； PDBConstruct 1–158； UniProt 45–202 Author chain E； PDBConstruct 1–158； UniProt 45–202

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	1yjg
Deposition date deposition_date	2005-01-14
Structure title title	Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)
Keywords keywords	helical bundle, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

1yjg__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1yjg__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yjg__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.83 Å
Rg (electron density)	19.68 Å
Total Rg	20.62 Å
Atom count	2246
Residues	312
Excluded volume	40564 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yjg__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yjg__assembly_2__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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1yjga_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
Family Family family	a.24.12.0 — automated matches

Domain ID domain_id	d1yjgb_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
Family Family family	a.24.12.0 — automated matches

Domain ID domain_id	d1yjgd_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
Family Family family	a.24.12.0 — automated matches

Domain ID domain_id	d1yjge_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.12 — Outer surface protein C (OspC)
Family Family family	a.24.12.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	1yjgA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	240 — Lipoprotein, type 6

Domain ID domain_id	1yjgB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	240 — Lipoprotein, type 6

Domain ID domain_id	1yjgD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	240 — Lipoprotein, type 6

Domain ID domain_id	1yjgE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	240 — Lipoprotein, type 6

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Unit-cell length a length_a	175.857 Å
Unit-cell length b length_b	34.213 Å
Unit-cell length c length_c	99.386 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.68 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	2.220 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2087
R_work r_work	0.2058
R_free r_free	0.2649

Description description	Surface protein VspA
Molecular weight formula_weight	16241.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,E
Atom count atom_count	4724

Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)

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

Surface protein VspA

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

1yjg__assembly_2__model_1

1yjg__assembly_2__model_1 | I(q)

1yjg__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Source organism organism	Borrelia turicatae
NCBI taxonomy ID ncbi_taxonomy_id	142
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	216

Variable Small Protein 1 of Borrelia turicatae (VspA or Vsp1)

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

Surface protein VspA

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

1yjg__assembly_2__model_1

1yjg__assembly_2__model_1 | I(q)

1yjg__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)