4jiv

VCA0105 PAAR-repeat protein from Vibrio cholerae in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5

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 4	Putative uncharacterized protein × 1 （Q9KN60） MAGNESIUM ION × 1 PALMITIC ACID × 1 STEARIC ACID × 1 Elaidic acid × 1 ZINC ION × 1 water × 4	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 5–96； UniProt 484–575 Author chain B； PDBConstruct 5–96； UniProt 484–575 Author chain C； PDBConstruct 5–96； UniProt 484–575

Putative uncharacterized protein

Vibrio cholerae O1 biovar eltor

UniProt Q9KN60

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Tail-associated lysozyme × 3 （P16009） MAGNESIUM ION × 1 PALMITIC ACID × 1 STEARIC ACID × 1 Elaidic acid × 1 ZINC ION × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KN60_VIBCH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–93； UniProt 2–94

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	4jiv
Deposition date deposition_date	2013-03-07
Structure title title	VCA0105 PAAR-repeat protein from Vibrio cholerae in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5
Keywords keywords	;PAAR-repeat motif, membrane piercing, type VI secretion system, Vibrio cholerae VgrG2, cell puncturing device, beta-helix, T4 gp5, VgrG tip, T6SS spike, HYDROLASE-PROTEIN BINDING complex ;; HYDROLASE/PROTEIN BINDING
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.

4jiv__assembly_1__model_1

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

Download this curve (.dat)

4jiv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4jiv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.30 Å
Rg (electron density)	26.49 Å
Total Rg	26.94 Å
Atom count	2727
Residues	372
Excluded volume	48176 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4jiv__assembly_1__model_1`	tetrameric （4）	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 (8)

Entity 1 Entity 1 polymer

Description description	Tail-associated lysozyme
Molecular weight formula_weight	9847.7 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	T566H, D568V, R571A, D573N, I574L, G575N
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	3393

GSGSGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYHIVGSAINLN

Source Source

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

Entity 2 Entity 2 polymer

Description description	Putative uncharacterized protein
Molecular weight formula_weight	9095.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GNGIVVGHLGTDHDGFPPTPVTAGSATVRYDGIPAARLGDPLAPHDKPKHPSHGRAIAAGSGTVMIDGKPAARVGDAVDCGGVLQGASSVNIG

Source Source

Source organism organism	Vibrio cholerae O1 biovar eltor
NCBI taxonomy ID ncbi_taxonomy_id	243277
Host organism host_organism	Escherichia coli

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	PALMITIC ACID
Molecular weight formula_weight	256.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	STEARIC ACID
Molecular weight formula_weight	284.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	Elaidic acid
Molecular weight formula_weight	282.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	453

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4jivD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	200 — Tumour Suppressor Smad4
Homologous superfamily homologous superfamily	60 —

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Unit-cell length a length_a	113.703 Å
Unit-cell length b length_b	113.703 Å
Unit-cell length c length_c	76.897 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	24

Space group space_group	P 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	1.903 Å
Low-resolution limit resolution_low	80.400 Å
R factor r_factor	0.1657
R_work r_work	0.1636
R_free r_free	0.2077

VCA0105 PAAR-repeat protein from Vibrio cholerae in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5

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

Putative uncharacterized 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

4jiv__assembly_1__model_1

4jiv__assembly_1__model_1 | I(q)

4jiv__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

VCA0105 PAAR-repeat protein from Vibrio cholerae in complex with a VgrG-like beta-helix that is based on a fragment of T4 gp5

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

Putative uncharacterized 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

4jiv__assembly_1__model_1

4jiv__assembly_1__model_1 | I(q)

4jiv__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 (8)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)