1h5w

2.1A Bacteriophage Phi-29 Connector

Method: X-RAY DIFFRACTION

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

UPPER COLLAR PROTEIN

BACTERIOPHAGE PHI-29

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 12	(4S)-2-METHYL-2,4-PENTANEDIOL × 16 water × 12	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

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	1h5w
Deposition date deposition_date	2001-05-28
Structure title title	2.1A Bacteriophage Phi-29 Connector
Keywords keywords	VIRUS, CONNECTOR, PORTAL, SH3-LIKE, HELIX BUNDLE; VIRUS
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.

1h5w__assembly_1__model_1

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

Download this curve (.dat)

1h5w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1h5w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.46 Å
Rg (electron density)	50.89 Å
Total Rg	51.16 Å
Atom count	24824
Residues	3032
Excluded volume	442120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1h5w__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 (3)

Entity 1 Entity 1 polymer

Description description	UPPER COLLAR PROTEIN
Molecular weight formula_weight	35917.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6700

MARKRSNTYRSINEIQRQKRNRWFIHYLNYLQSLAYQLFEWENLPPTINPSFLEKSIHQFGYVGFYKDPVISYIACNGALSGQRDVYNQATVFRAASPVYQKEFKLYNYRDMKEEDMGVVIYNNDMAFPTTPTLELFAAELAELKEIISVNQNAQKTPVLIRANDNNQLSLKQVYNQYEGNAPVIFAHEALDSDSIEVFKTDAPYVVDKLNAQKNAVWNEMMTFLGIKNANLEKKERMVTDEVSSNDEQIESSGTVFLKSREEACEKINELYGLNVKVKFRYDIVEQMRRELQQIENVSRGTSDGETNE

Source Source

Source organism organism	BACTERIOPHAGE PHI-29
NCBI taxonomy ID ncbi_taxonomy_id	10756
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	494

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1h5wa_
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	d1h5wb_
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	d1h5wc_
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 (9 domains)

Domain ID domain_id	1h5wA01
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	1h5wA02
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	1h5wA03
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	1h5wB01
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	1h5wB02
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	1h5wB03
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	1h5wC01
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	1h5wC02
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	1h5wC03
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	155.340 Å
Unit-cell length b length_b	155.340 Å
Unit-cell length c length_c	160.430 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	48

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	42.000 Å
R factor r_factor	0.2050
R_work r_work	0.2050
R_free r_free	0.2520

2.1A Bacteriophage Phi-29 Connector

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

1h5w__assembly_1__model_1

1h5w__assembly_1__model_1 | I(q)

1h5w__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) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

2.1A Bacteriophage Phi-29 Connector

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

1h5w__assembly_1__model_1

1h5w__assembly_1__model_1 | I(q)

1h5w__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) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)