6p22

Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC

Method: X-RAY DIFFRACTION

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

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN × 1 （Q7N648） MAGNESIUM ION × 1 STEARIC ACID × 1 Elaidic acid × 1 PALMITIC ACID × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BP5_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–86； UniProt 484–565 Author chain B； PDBConstruct 5–86； UniProt 484–565 Author chain C； PDBConstruct 5–86； UniProt 484–565

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

UniProt Q7N647

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN × 1 （Q7N648） MAGNESIUM ION × 1 STEARIC ACID × 1 Elaidic acid × 1 PALMITIC ACID × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7N647_PHOLL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 87–97； UniProt 523–533 Author chain B； PDBConstruct 87–97； UniProt 523–533 Author chain C； PDBConstruct 87–97； UniProt 523–533

PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN

Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

UniProt Q7N648

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC × 3 （P16009,Q7N647） MAGNESIUM ION × 1 STEARIC ACID × 1 Elaidic acid × 1 PALMITIC ACID × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7N648_PHOLL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–138； UniProt 1–138

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	6p22
Deposition date deposition_date	2019-05-20
Structure title title	Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC
Keywords keywords	;PVC, Photorhabdus laumondii, membrane piercing, central spike, cell puncturing device, PAAR-repeat motif, beta helix, T4 gp5, contractile injection system, viral protein, Pvc8, Pvc10, hydrolase ;; 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.

6p22__assembly_1__model_1

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

Download this curve (.dat)

6p22__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6p22__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.93 Å
Rg (electron density)	30.78 Å
Total Rg	30.90 Å
Atom count	6301
Residues	419
Excluded volume	56007 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6p22__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 (7)

Entity 1 Entity 1 polymer

Description description	CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC
Molecular weight formula_weight	10011.9 kDa
EC 编号 ec_number	3.2.1.17
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	6455

GSGSGDETKTVEGNGTILVKGNVTIIVEGNADITVKGDATTLVEGNQTNTVNGNLSWKVAGTVDWDVGGDWTEKMASMSSISSGQYDIKGAKINLTQ

Source Source

Source organism organism	Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
NCBI taxonomy ID ncbi_taxonomy_id	243265
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PAAR-REPEAT CENTRAL SPIKE TIP PROTEIN
Molecular weight formula_weight	14669.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSKQLVIDGDNLLFEPLFGNRQVTILGPATIRGSGHAKIQGKKIVIVGDEKKVQLQAQYITPSHPIPGMGIVTIAQLDANQQVNFCRTPATAIVVGQQFIARFTPTQPANNPSTGPDVTTPSMGKGRFIASQYAVSAG

Source Source

Source organism organism	Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
NCBI taxonomy ID ncbi_taxonomy_id	243265
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	STEARIC ACID
Molecular weight formula_weight	284.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

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Unit-cell length a length_a	34.305 Å
Unit-cell length b length_b	56.963 Å
Unit-cell length c length_c	222.994 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.291 Å
Low-resolution limit resolution_low	45.213 Å
R factor r_factor	0.1840
R_work r_work	0.1819
R_free r_free	0.2224

Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC

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

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

State in the Current Structure

Other States of the Same Protein in the Database

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

State in the Current Structure

Other States of the Same Protein in the Database

PAAR-REPEAT CENTRAL SPIKE TIP 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

6p22__assembly_1__model_1

6p22__assembly_1__model_1 | I(q)

6p22__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 (7)

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 water

7. Citations (3)

Photorhabdus Virulence Cassette (PVC) PAAR repeat protein Pvc10 in complex with a T4 gp5 beta-helix fragment modified to mimic Pvc8, the central spike protein of PVC

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

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CHIMERA OF CENTRAL SPIKE PROTEINS GP5 FROM PHAGE T4 AND PVC8 FROM PVC

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PAAR-REPEAT CENTRAL SPIKE TIP 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

6p22__assembly_1__model_1

6p22__assembly_1__model_1 | I(q)

6p22__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 (7)

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 water

7. Citations (3)