SAXSdb — 2fio

▼

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

Late genes activator

Bacillus phage phi29

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	DNA (41-MER) × 1 DNA (41-MER) × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VG4_BPPH2
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 2–124 Author chain B； PDBConstruct 1–123； UniProt 2–124

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2fio
Deposition date deposition_date	2005-12-30
Structure title title	Phage phi29 transcription regulator p4-DNA complex
Keywords keywords	PROTEIN-DNA COMPLEX; N-HOOK DNA-BINDING MOTIF; TRANSCRIPTION REGULATION, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2fio__assembly_1__model_1

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

Download this curve (.dat)

2fio__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fio__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.69 Å
Rg (electron density)	32.30 Å
Total Rg	32.78 Å
Atom count	3691
Residues	318
Excluded volume	60534 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fio__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA (41-MER)
Molecular weight formula_weight	12641.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	3777

AAAAACGTCAACATTTTATAAAAAAGTCTTGCAAAAAGTTA

Entity 2 Entity 2 polymer

Description description	DNA (41-MER)
Molecular weight formula_weight	12591.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TAACTTTTTGCAAGACTTTTTTATAAAATGTTGACGTTTTT

Entity 3 Entity 3 polymer

Description description	Late genes activator
Molecular weight formula_weight	14929.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

PKTQRGIYHNLKESEYVASNTDVTFFFSSELYLNKFLDGYQEYRKKFNKKIERVAVTPWNMDMLADITFYSEVEKRGFHAWLKGDNATWREVHVYALRIMTKPNTLDWSRIQKPRLRERRKSM

Source Source

Source organism organism	Bacillus phage phi29
NCBI taxonomy ID ncbi_taxonomy_id	10756
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2fioA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3560 — Phi-29-like late genes activator, P4

Domain ID domain_id	2fioB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	3560 — Phi-29-like late genes activator, P4

▶

Unit-cell length a length_a	52.400 Å
Unit-cell length b length_b	27.800 Å
Unit-cell length c length_c	192.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2320
R_work r_work	0.2290
R_free r_free	0.2790

Phage phi29 transcription regulator p4-DNA complex

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

Late genes activator

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

2fio__assembly_1__model_1

2fio__assembly_1__model_1 | I(q)

2fio__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Phage phi29 transcription regulator p4-DNA complex

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

Late genes activator

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

2fio__assembly_1__model_1

2fio__assembly_1__model_1 | I(q)

2fio__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)