1k28

The Structure of the Bacteriophage T4 Cell-Puncturing Device

Method: X-RAY DIFFRACTION

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

TAIL-ASSOCIATED LYSOZYME

Enterobacteria phage T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	BASEPLATE STRUCTURAL PROTEIN GP27 × 3 （P17172） POTASSIUM ION × 3 PHOSPHATE ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VG05_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–575； UniProt 1–575

BASEPLATE STRUCTURAL PROTEIN GP27

Enterobacteria phage T4

UniProt P17172

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	TAIL-ASSOCIATED LYSOZYME × 3 （P16009） POTASSIUM ION × 3 PHOSPHATE ION × 3 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VG27_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–391； UniProt 1–391

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	1k28
Deposition date deposition_date	2001-09-26
Structure title title	The Structure of the Bacteriophage T4 Cell-Puncturing Device
Keywords keywords	Triple-stranded beta-helix, OB fold, pseudohexamer, T4 tail lysozyme, HUB, gp27-gp5*-gp5C, HYDROLASE-STRUCTURAL PROTEIN COMPLEX; HYDROLASE/STRUCTURAL 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.

1k28__assembly_1__model_1

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

Download this curve (.dat)

1k28__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k28__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.52 Å
Rg (electron density)	52.89 Å
Total Rg	52.92 Å
Atom count	21669
Residues	2718
Excluded volume	383520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k28__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 (5)

Entity 1 Entity 1 polymer

Description description	TAIL-ASSOCIATED LYSOZYME
Molecular weight formula_weight	64313.9 kDa
EC 编号 ec_number	3.2.1.17
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	7614

MEMISNNLNWFVGVVEDRMDPLKLGRVRVRVVGLHPPQRAQGDVMGIPTEKLPWMSVIQPITSAAMSGIGGSVTGPVEGTRVYGHFLDKWKTNGIVLGTYGGIVREKPNRLEGFSDPTGQYPRRLGNDTNVLNQGGEVGYDSSSNVIQDSNLDTAINPDDRPLSEIPTDDNPNMSMAEMLRRDEGLRLKVYWDTEGYPTIGIGHLIMKQPVRDMAQINKVLSKQVGREITGNPGSITMEEATTLFERDLADMQRDIKSHSKVGPVWQAVNRSRQMALENMAFQMGVGGVAKFNTMLTAMLAGDWEKAYKAGRDSLWYQQTKGRASRVTMIILTGNLESYGVEVKTPARSLSAMAATVAKSSDPADPPIPNDSRILFKEPVSSYKGEYPYVHTMETESGHIQEFDDTPGQERYRLVHPTGTYEEVSPSGRRTRKTVDNLYDITNADGNFLVAGDKKTNVGGSEIYYNMDNRLHQIDGSNTIFVRGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYTIDGSRIDIGSVDHHHHHH

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	BASEPLATE STRUCTURAL PROTEIN GP27
Molecular weight formula_weight	45228.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSMLQRPGYPNLSVKLFDSYDAWSNNRFVELAATITTLTMRDSLYGRNEGMLQFYDSKNIHTKMDGNEIIQISVANANDINNVKTRIYGCKHFSVSVDSKGDNIIAIELGTIHSIENLKFGRPFFPDAGESIKEMLGVIYQDRTLLTPAINAINAYVPDIPWTSTFENYLSYVREVALAVGSDKFVFVWQDIMGVNMMDYDMMINQEPYPMIVGEPSLIGQFIQELKYPLAYDFVWLTKSNPHKRDPMKNATIYAHSFLDSSIPMITTGKGENSIVVSRSGAYSEMTYRNGYEEAIRLQTMAQYDGYAKCSTIGNFNLTPGVKIIFNDSKNQFKTEFYVDEVIHELSNNNSVTHLYMFTNATKLETIDPVKVKNEFKSDTTTEESSSSNKQ

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	389

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1k28a1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.8 — gp5 N-terminal domain-like
Family Family family	b.40.8.1 — gp4 N-terminal domain-like

Domain ID domain_id	d1k28a2
Class class	b — All beta proteins
Fold Fold fold	b.108 — Triple-stranded beta-helix
Superfamily Superfamily superfamily	b.108.1 — Phage fibre proteins
Family Family family	b.108.1.2 — Tail-associated lysozyme gp5, C-terminal domain

Domain ID domain_id	d1k28a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.3 — Phage lysozyme

Domain ID domain_id	d1k28a4
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1k28d1
Class class	b — All beta proteins
Fold Fold fold	b.106 — Phage tail proteins
Superfamily Superfamily superfamily	b.106.1 — Phage tail proteins
Family Family family	b.106.1.1 — Baseplate protein-like

Domain ID domain_id	d1k28d2
Class class	b — All beta proteins
Fold Fold fold	b.106 — Phage tail proteins
Superfamily Superfamily superfamily	b.106.1 — Phage tail proteins
Family Family family	b.106.1.1 — Baseplate protein-like

CATH v4.4 (7 domains)

Domain ID domain_id	1k28A01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	260 — Nucleic acid-binding protein domain

Domain ID domain_id	1k28A02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	190 —

Domain ID domain_id	1k28A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1k28D01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1k28D02
Class class	3 — Alpha Beta
Architecture architecture	55 — 3-Layer(bab) Sandwich
Topology topology	50 — Phage tail protein beta-alpha-beta fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1k28D03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	150 — Bacteriophage T4, Gp27, baseplate hub, domain 3

Domain ID domain_id	1k28D04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	139.261 Å
Unit-cell length b length_b	139.261 Å
Unit-cell length c length_c	381.998 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	2.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2140
R_work r_work	0.2110
R_free r_free	0.2800

The Structure of the Bacteriophage T4 Cell-Puncturing Device

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

TAIL-ASSOCIATED LYSOZYME

State in the Current Structure

Other States of the Same Protein in the Database

BASEPLATE STRUCTURAL PROTEIN GP27

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

1k28__assembly_1__model_1

1k28__assembly_1__model_1 | I(q)

1k28__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

CATH v4.4 (7 domains)

7. Citations (1)

The Structure of the Bacteriophage T4 Cell-Puncturing Device

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

TAIL-ASSOCIATED LYSOZYME

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

BASEPLATE STRUCTURAL PROTEIN GP27

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

1k28__assembly_1__model_1

1k28__assembly_1__model_1 | I(q)

1k28__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

CATH v4.4 (7 domains)

7. Citations (1)