SAXSdb — 3gq7

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

Preneck appendage 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 3	CALCIUM ION × 3 MAGNESIUM ION × 3 PHOSPHATE ION × 3 CARBONATE ION × 3 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	CALCIUM ION × 6 MAGNESIUM ION × 6 PHOSPHATE ION × 6 CARBONATE ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3VMP8_BPPH2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–609； UniProt 89–691

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	3gq7
Deposition date deposition_date	2009-03-24
Structure title title	Crystal Structure of the Bacteriophage Phi29 Gene Product 12 N-terminal Fragment
Keywords keywords	beta helix, 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.

3gq7__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3gq7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gq7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	76.77 Å
Rg (electron density)	77.98 Å
Total Rg	77.70 Å
Atom count	26994
Residues	3630
Excluded volume	471830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gq7__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gq7__assembly_2__model_1`	hexameric （6）	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 (6)

Entity 1 Entity 1 polymer

Description description	Preneck appendage protein
Molecular weight formula_weight	64410.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4997

HHHHHHFADLVIQVIDELKQFGVSVKTYGAKGDGVTDDIRAFEKAIESGFPVYVPYGTFMVSRGIKLPSNTVLTGAGKRNAVIRFMDSVGRGESLMYNENVTTGNENIFLSSFTLDGNNKRLGQGISGIGGSRESNLSIRACHNVYIRDIEAVDCTLHGIDITCGGLDYPYLGDGTTAPNPSENIWIENCEATGFGDDGITTHHSQYINILNCYSHDPRLTANCNGFEIDDGSRHVVLSNNRSKGCYGGIEIKAHGDAPAAYNISINGHMSVEDVRSYNFRHIGHHAATAPQSVSAKNIVASNLVSIRPNNKRGFQDNATPRVLAVSAYYGVVINGLTGYTDDPNLLTETVVSVQFRARNCSLNGVVLTGFSNSENGIYVIGGSRGGDAVNISNVTLNNSGRYGVSIGSGIENVSITNISGIGDGINSPVALVSTINSNPEISGLSSIGYPTVARVAGTDYNDGLTLFNGAFRASTTSSGKIHSEGFIMGSTSGCEASVSKSGVLTSSSSKTSSERSLIAGSSTSEAKGTYNTILGSLGAVADEQFAALISASQSRASGNHNLILSSYGINTTGSYKVNGGFEKINWELDSLNGRIKARDTVTGGNTWS

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 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	CARBONATE ION
Molecular weight formula_weight	60.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	439

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3gq7A01
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

Domain ID domain_id	3gq7A02
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	10 — UDP N-Acetylglucosamine Acyltransferase; domain 1
Homologous superfamily homologous superfamily	20 — Insect antifreeze protein

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Unit-cell length a length_a	89.879 Å
Unit-cell length b length_b	89.879 Å
Unit-cell length c length_c	585.440 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	43.810 Å
R factor r_factor	0.1590
R_work r_work	0.1580
R_free r_free	0.1900

Crystal Structure of the Bacteriophage Phi29 Gene Product 12 N-terminal Fragment

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

Preneck appendage 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

3gq7__assembly_2__model_1

3gq7__assembly_2__model_1 | I(q)

3gq7__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the Bacteriophage Phi29 Gene Product 12 N-terminal Fragment

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

Preneck appendage 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

3gq7__assembly_2__model_1

3gq7__assembly_2__model_1 | I(q)

3gq7__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)