1jnb

CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29

Method: X-RAY DIFFRACTION

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

UPPER COLLAR PROTEIN

Bacillus phage phi29

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VG10_BPPH2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–309； UniProt 1–309 Author chain B； PDBConstruct 1–309； UniProt 1–309 Author chain C； PDBConstruct 1–309； UniProt 1–309 Author chain D； PDBConstruct 1–309； UniProt 1–309 Author chain E； PDBConstruct 1–309； UniProt 1–309 Author chain F； PDBConstruct 1–309； UniProt 1–309 Author chain G； PDBConstruct 1–309； UniProt 1–309 Author chain H； PDBConstruct 1–309； UniProt 1–309 Author chain I； PDBConstruct 1–309； UniProt 1–309 Author chain J； PDBConstruct 1–309； UniProt 1–309 Author chain K； PDBConstruct 1–309； UniProt 1–309 Author chain L； PDBConstruct 1–309； UniProt 1–309

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	1jnb
Deposition date deposition_date	2001-07-23
Structure title title	CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29
Keywords keywords	helix bundle, Viral protein; VIRAL 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.

1jnb__assembly_1__model_1

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

Download this curve (.dat)

1jnb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jnb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.21 Å
Rg (electron density)	50.59 Å
Total Rg	50.88 Å
Atom count	25236
Residues	3084
Excluded volume	449460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jnb__assembly_1__model_1`	dodecameric （12）	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 (1)

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1jnba_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbd_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbe_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbf_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbg_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbh_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbi_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbj_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbk_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	d1jnbl_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.27 — Upper collar protein gp10 (connector protein)
Superfamily Superfamily superfamily	e.27.1 — Upper collar protein gp10 (connector protein)
Family Family family	e.27.1.1 — Upper collar protein gp10 (connector protein)

CATH v4.4 (36 domains)

Domain ID domain_id	1jnbA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbE02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbE03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbF02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbF03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbG02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbG03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbH02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbH03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbI02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbI03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbJ02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbJ03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbK01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbK02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbK03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

Domain ID domain_id	1jnbL01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1jnbL02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	500 — Upper collar protein gp10 (connector protein) fold
Homologous superfamily homologous superfamily	10 — Upper collar protein gp10 (connector protein)

Domain ID domain_id	1jnbL03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1350 — Crambin
Homologous superfamily homologous superfamily	20 — Bacteriophage PHI-29 conector. Domain 3

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Unit-cell length a length_a	177.160 Å
Unit-cell length b length_b	169.240 Å
Unit-cell length c length_c	185.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

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

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	9.000 Å
R factor r_factor	0.2866
R_work r_work	0.2844
R_free r_free	0.3014

Description description	UPPER COLLAR PROTEIN
Molecular weight formula_weight	35917.3 kDa
Source method src_method	man
Copy count entity_count	12

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	25236

CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29

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

UPPER COLLAR PROTEIN

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

1jnb__assembly_1__model_1

1jnb__assembly_1__model_1 | I(q)

1jnb__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (12 domains)

CATH v4.4 (36 domains)

7. Citations (2)

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

CONNECTOR PROTEIN FROM BACTERIOPHAGE PHI29

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

UPPER COLLAR PROTEIN

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

1jnb__assembly_1__model_1

1jnb__assembly_1__model_1 | I(q)

1jnb__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (12 domains)

CATH v4.4 (36 domains)

7. Citations (2)