SAXSdb — 5muw

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

Packaging enzyme P4

Pseudomonas phage phi6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	CALCIUM ION × 6 ADENOSINE-5'-DIPHOSPHATE × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P4_BPPH6
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 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	5muw
Deposition date deposition_date	2017-01-14
Structure title title	Atomic structure of P4 packaging enzyme fitted into a localized reconstruction of bacteriophage phi6 vertex
Keywords keywords	packaging, ATPase, vertex, hyrdolase, HYDROLASE; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

5muw__assembly_1__model_1

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

Download this curve (.dat)

5muw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5muw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.84 Å
Rg (electron density)	35.98 Å
Total Rg	36.51 Å
Atom count	12234
Residues	1621
Excluded volume	220130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5muw__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Packaging enzyme P4
Molecular weight formula_weight	32678.7 kDa
EC 编号 ec_number	3.6.1.15
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,I,J,K,L
Atom count atom_count	12234

MPIVVTQAHIDRVGIAADLLDASPVSLQVLGRPTAINTVVIKTYIAAVMELASKQGGSLAGVDIRPSVLLKDTAIFTKPKAKSADVESDVDVLDTGIYSVPGLARKPVTHRWPSEGIYSGVTALMGATGSGKSITLNEKLRPDVLIRWGEVAEAYDELDTAVHISTLDEMLIVCIGLGALGFNVAVDSVRPLLFRLKGAASAGGIVAVFYSLLTDISNLFTQYDCSVVMVVNPMVDAEKIEYVFGQVMASTVGAILCADGNVSRTMFRTNKGRIFNGAAPLAADTHMPSMDRPTSMKALDHTSIASVAP

Source Source

Source organism organism	Pseudomonas phage phi6
NCBI taxonomy ID ncbi_taxonomy_id	10879
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	6

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5muwA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5muwB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5muwI01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5muwJ01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5muwK01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5muwL01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	9.100 Å
Low-resolution limit resolution_low	9.100 Å
R factor r_factor	0.2183
R_work r_work	0.2170
R_free r_free	0.2441

Resolution resolution	9.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	56448

Atomic structure of P4 packaging enzyme fitted into a localized reconstruction of bacteriophage phi6 vertex

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

Packaging enzyme P4

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

5muw__assembly_1__model_1

5muw__assembly_1__model_1 | I(q)

5muw__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

冷冻电镜 EM 3D

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 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)

Atomic structure of P4 packaging enzyme fitted into a localized reconstruction of bacteriophage phi6 vertex

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

Packaging enzyme P4

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

5muw__assembly_1__model_1

5muw__assembly_1__model_1 | I(q)

5muw__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

冷冻电镜 EM 3D

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 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)