SAXSdb — 1vp7

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

exodeoxyribonuclease VII small subunit

Bordetella pertussis Tohama I

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
3	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	EX7S_BORPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–100； UniProt 1–88 Author chain B； PDBConstruct 13–100； UniProt 1–88 Author chain C； PDBConstruct 13–100； UniProt 1–88 Author chain D； PDBConstruct 13–100； UniProt 1–88 Author chain E； PDBConstruct 13–100； UniProt 1–88 Author chain F； PDBConstruct 13–100； UniProt 1–88

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	1vp7
Deposition date deposition_date	2004-10-14
Structure title title	Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution
Keywords keywords	;NP_881400.1, Exodeoxyribonuclease VII small subunit E.C.3.1.11.6, structural genomics, Joint Center for Structural Genomics, JCSG, PSI, Protein Structure Initiative, HYDROLASE ;; HYDROLASE
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.

1vp7__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1vp7__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vp7__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.22 Å
Rg (electron density)	19.17 Å
Total Rg	19.98 Å
Atom count	976
Residues	130
Excluded volume	17464 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vp7__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1vp7__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1vp7__assembly_3__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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1vp7a_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.13 — XseB-like
Family Family family	a.7.13.1 — XseB-like

Domain ID domain_id	d1vp7b_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.13 — XseB-like
Family Family family	a.7.13.1 — XseB-like

Domain ID domain_id	d1vp7c_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.13 — XseB-like
Family Family family	a.7.13.1 — XseB-like

Domain ID domain_id	d1vp7d_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.13 — XseB-like
Family Family family	a.7.13.1 — XseB-like

Domain ID domain_id	d1vp7e_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.13 — XseB-like
Family Family family	a.7.13.1 — XseB-like

Domain ID domain_id	d1vp7f_
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.13 — XseB-like
Family Family family	a.7.13.1 — XseB-like

CATH v4.4 (6 domains)

Domain ID domain_id	1vp7A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1040 — Exonuclease VII, small subunit

Domain ID domain_id	1vp7B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1040 — Exonuclease VII, small subunit

Domain ID domain_id	1vp7C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1040 — Exonuclease VII, small subunit

Domain ID domain_id	1vp7D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1040 — Exonuclease VII, small subunit

Domain ID domain_id	1vp7E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1040 — Exonuclease VII, small subunit

Domain ID domain_id	1vp7F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	1040 — Exonuclease VII, small subunit

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Unit-cell length a length_a	107.030 Å
Unit-cell length b length_b	107.030 Å
Unit-cell length c length_c	207.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	72

Space group space_group	P 6 2 2
Space-group number int_tables_number	177
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	29.020 Å
R factor r_factor	0.2047
R_work r_work	0.2027
R_free r_free	0.2444

Description description	exodeoxyribonuclease VII small subunit
Molecular weight formula_weight	11232.0 kDa
EC 编号 ec_number	3.1.11.6
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	3262

Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution

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

exodeoxyribonuclease VII small subunit

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

1vp7__assembly_3__model_1

1vp7__assembly_3__model_1 | I(q)

1vp7__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Bordetella pertussis Tohama I
NCBI taxonomy ID ncbi_taxonomy_id	257313
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution

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

exodeoxyribonuclease VII small subunit

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

1vp7__assembly_3__model_1

1vp7__assembly_3__model_1 | I(q)

1vp7__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)