SAXSdb — 4dwl

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

Bbp7

Bordetella phage BPP-1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 5	PHOSPHATE ION × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q775D7_BPBPP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–131； UniProt 1–128 Author chain B； PDBConstruct 4–131； UniProt 1–128 Author chain C； PDBConstruct 4–131； UniProt 1–128 Author chain D； PDBConstruct 4–131； UniProt 1–128 Author chain E； PDBConstruct 4–131； UniProt 1–128

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	4dwl
Deposition date deposition_date	2012-02-24
Structure title title	Avd molecule from Bordetella bacteriophage DGR
Keywords keywords	;pentameric four helix bundle, Accessory variability determinant from Bordetella bacteriophage diversity generating retroelements, Reverse Transcriptase, phosphate binding protein, nucleic acid binding protein ;; nucleic acid 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.

4dwl__assembly_1__model_1

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

Download this curve (.dat)

4dwl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4dwl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.45 Å
Rg (electron density)	24.21 Å
Total Rg	24.93 Å
Atom count	4333
Residues	526
Excluded volume	79001 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4dwl__assembly_1__model_1`	pentameric （5）	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	Bbp7
Molecular weight formula_weight	15008.8 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,C,D
Atom count atom_count	4394

GSHMEPIEEATKCYDQMLIVERYERVISYLYPIAQSIPRKHGVAREMFLKCLLGQVELFIVAGKSNQVSKLYAADAGLAMLRFWLRFLAGIQKPHAMTPHQVETAQVLIAEVGRILGSWIARVNRKGQAGK

Source Source

Source organism organism	Bordetella phage BPP-1
NCBI taxonomy ID ncbi_taxonomy_id	194699
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	4dwlA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	60 — 23S rRNA-intervening sequence

Domain ID domain_id	4dwlB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	60 — 23S rRNA-intervening sequence

Domain ID domain_id	4dwlC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	60 — 23S rRNA-intervening sequence

Domain ID domain_id	4dwlD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	60 — 23S rRNA-intervening sequence

Domain ID domain_id	4dwlE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1440 — de novo design (two linked rop proteins)
Homologous superfamily homologous superfamily	60 — 23S rRNA-intervening sequence

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Unit-cell length a length_a	54.317 Å
Unit-cell length b length_b	63.072 Å
Unit-cell length c length_c	105.295 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.690 Å
Low-resolution limit resolution_low	42.910 Å
R factor r_factor	0.1970
R_work r_work	0.1944
R_free r_free	0.2439

Avd molecule from Bordetella bacteriophage DGR

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

Bbp7

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

4dwl__assembly_1__model_1

4dwl__assembly_1__model_1 | I(q)

4dwl__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) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

Avd molecule from Bordetella bacteriophage DGR

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

Bbp7

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

4dwl__assembly_1__model_1

4dwl__assembly_1__model_1 | I(q)

4dwl__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) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)