SAXSdb — 2vic

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

TRANSPOSASE ORFA

HELICOBACTER PYLORI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;5'-D(APAPAPGPCPCPCPCPTPAP GPCPTPTPTPTPAPGPCPTPAPTPGPGPGPG)-3' ; × 2 MANGANESE (II) ION × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q933Z0_HELPY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–159； UniProt 2–155 Author chain B； PDBConstruct 6–159； UniProt 2–155

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	2vic
Deposition date deposition_date	2007-11-29
Structure title title	CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX with Left end 26- mer DNA and manganese
Keywords keywords	DNA-BINDING PROTEIN, PROTEIN-DNA COMPLEX, HUH MOTIF, DNA STEM LOOP, TRANSPOSITION, DNA BINDING PROTEIN; DNA BINDING 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.

2vic__assembly_1__model_1

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

Download this curve (.dat)

2vic__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vic__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.37 Å
Rg (electron density)	22.41 Å
Total Rg	23.14 Å
Atom count	3316
Residues	330
Excluded volume	56290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vic__assembly_1__model_1`	tetrameric （4）	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	TRANSPOSASE ORFA
Molecular weight formula_weight	18392.4 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	3427

GSAMASNAVLYKSNHNVVYSCKYHIVWCPKYRRKVLVGAVEMRLKEIIQEVAKELRVEIIEMQTDKDHIHILADIDPSFGVMKFIKTAKGRSSRILRQEFNHLKTKLPTLWTNSCFISTVGGAPLNVVKQYIENQQNSNRPKQKEKWKSYVDNLQTKAL

Source Source

Source organism organism	HELICOBACTER PYLORI
NCBI taxonomy ID ncbi_taxonomy_id	210
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	;5'-D(APAPAPGPCPCPCPCPTPAP GPCPTPTPTPTPAPGPCPTPAPTPGPGPGPG)-3' ;
Molecular weight formula_weight	8003.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D

AAAGCCCCTAGCTTTTAGCTATGGGG

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 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	111

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vica1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.57 — Transposase IS200-like
Family Family family	d.58.57.1 — Transposase IS200-like

Domain ID domain_id	d2vicb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.57 — Transposase IS200-like
Family Family family	d.58.57.1 — Transposase IS200-like

CATH v4.4 (2 domains)

Domain ID domain_id	2vicA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

Domain ID domain_id	2vicB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1290 — Transposase IS200-like

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Unit-cell length a length_a	74.206 Å
Unit-cell length b length_b	50.261 Å
Unit-cell length c length_c	115.625 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	19.470 Å
R factor r_factor	0.2030
R_work r_work	0.2030
R_free r_free	0.2410

CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX with Left end 26- mer DNA and manganese

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

TRANSPOSASE ORFA

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

2vic__assembly_1__model_1

2vic__assembly_1__model_1 | I(q)

2vic__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE ISHP608 TRANSPOSASE IN COMPLEX with Left end 26- mer DNA and manganese

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

TRANSPOSASE ORFA

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

2vic__assembly_1__model_1

2vic__assembly_1__model_1 | I(q)

2vic__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)