2c5r

The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA

Method: X-RAY DIFFRACTION

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

EARLY PROTEIN P16.7

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 6 DNA 2	5'-D(TPCPCPAPCPCPGPGP)-3' × 1 5'-D(CPCPGPGPTPGPGPAP)-3' × 1 water × 7	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VG167_BPPH2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–67； UniProt 64–130 Author chain B； PDBConstruct 1–67； UniProt 64–130 Author chain C； PDBConstruct 1–67； UniProt 64–130 Author chain D； PDBConstruct 1–67； UniProt 64–130 Author chain E； PDBConstruct 1–67； UniProt 64–130 Author chain F； PDBConstruct 1–67； UniProt 64–130

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	2c5r
Deposition date deposition_date	2005-10-31
Structure title title	The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA
Keywords keywords	DNA-BINDING PROTEIN-DNA COMPLEX, DNA-BINDING PROTEIN, COMPLEX (DNA-BINDING PROTEIN-DNA); DNA-BINDING PROTEIN/DNA
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.

2c5r__assembly_1__model_1

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

Download this curve (.dat)

2c5r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c5r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.66 Å
Rg (electron density)	23.68 Å
Total Rg	24.59 Å
Atom count	3484
Residues	400
Excluded volume	60685 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c5r__assembly_1__model_1`	octameric （8）	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	EARLY PROTEIN P16.7
Molecular weight formula_weight	7938.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	3535

KTVNLSACEVAVLDLYEQSNIRIPSDIIEDLVNQRLQSEQEVLNYIETQRTYWKLENQKKLYRGSLK

Source Source

Source organism organism	BACILLUS PHAGE PHI29
NCBI taxonomy ID ncbi_taxonomy_id	10756
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	5'-D(TPCPCPAPCPCPGPGP)-3'
Molecular weight formula_weight	2387.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

TCCACCGG

Entity 3 Entity 3 polymer

Description description	5'-D(CPCPGPGPTPGPGPAP)-3'
Molecular weight formula_weight	2467.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Z

CCGGTGGA

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2c5ra1
Class class	a — All alpha proteins
Fold Fold fold	a.251 — Phage replication organizer domain
Superfamily Superfamily superfamily	a.251.1 — Phage replication organizer domain
Family Family family	a.251.1.1 — Phage replication organizer domain

Domain ID domain_id	d2c5rb_
Class class	a — All alpha proteins
Fold Fold fold	a.251 — Phage replication organizer domain
Superfamily Superfamily superfamily	a.251.1 — Phage replication organizer domain
Family Family family	a.251.1.1 — Phage replication organizer domain

Domain ID domain_id	d2c5rc_
Class class	a — All alpha proteins
Fold Fold fold	a.251 — Phage replication organizer domain
Superfamily Superfamily superfamily	a.251.1 — Phage replication organizer domain
Family Family family	a.251.1.1 — Phage replication organizer domain

Domain ID domain_id	d2c5rd_
Class class	a — All alpha proteins
Fold Fold fold	a.251 — Phage replication organizer domain
Superfamily Superfamily superfamily	a.251.1 — Phage replication organizer domain
Family Family family	a.251.1.1 — Phage replication organizer domain

Domain ID domain_id	d2c5re_
Class class	a — All alpha proteins
Fold Fold fold	a.251 — Phage replication organizer domain
Superfamily Superfamily superfamily	a.251.1 — Phage replication organizer domain
Family Family family	a.251.1.1 — Phage replication organizer domain

Domain ID domain_id	d2c5rf_
Class class	a — All alpha proteins
Fold Fold fold	a.251 — Phage replication organizer domain
Superfamily Superfamily superfamily	a.251.1 — Phage replication organizer domain
Family Family family	a.251.1.1 — Phage replication organizer domain

CATH v4.4 (6 domains)

Domain ID domain_id	2c5rA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

Domain ID domain_id	2c5rB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

Domain ID domain_id	2c5rC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

Domain ID domain_id	2c5rD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

Domain ID domain_id	2c5rE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

Domain ID domain_id	2c5rF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	600 — Phage phi29 replication organiser protein p16.7-like

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Unit-cell length a length_a	65.505 Å
Unit-cell length b length_b	72.111 Å
Unit-cell length c length_c	127.360 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2540
R_work r_work	0.2510
R_free r_free	0.2920

The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA

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

EARLY PROTEIN P16.7

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

2c5r__assembly_1__model_1

2c5r__assembly_1__model_1 | I(q)

2c5r__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 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The structure of phage phi29 replication organizer protein p16.7 in complex with double stranded DNA

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

EARLY PROTEIN P16.7

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

2c5r__assembly_1__model_1

2c5r__assembly_1__model_1 | I(q)

2c5r__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 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)