SAXSdb — 4iyc

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

LukS-PV

Staphylococcus phage PVL

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O80066_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–292； UniProt 29–312 Author chain B； PDBConstruct 9–292； UniProt 29–312 Author chain C； PDBConstruct 9–292； UniProt 29–312 Author chain D； PDBConstruct 9–292； UniProt 29–312

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	4iyc
Deposition date deposition_date	2013-01-28
Structure title title	Structure of the T244A mutant of the PANTON-VALENTINE LEUCOCIDIN component from STAPHYLOCOCCUS AUREUS
Keywords keywords	Staphylococcus aureus, S component leucocidin, bi-component leucotoxin, beta-barrel pore forming toxin, TOXIN; TOXIN
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.

4iyc__assembly_2__model_1

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

Download this curve (.dat)

4iyc__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4iyc__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.84 Å
Rg (electron density)	22.14 Å
Total Rg	22.83 Å
Atom count	2193
Residues	278
Excluded volume	38330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4iyc__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4iyc__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4iyc__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4iyc__assembly_4__model_1`	monomeric （1）	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 (2)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4iyca_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

Domain ID domain_id	d4iycb_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

Domain ID domain_id	d4iycc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

Domain ID domain_id	d4iycd_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.6 — Leukocidin-like
Superfamily Superfamily superfamily	f.6.1 — Leukocidin-like
Family Family family	f.6.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	4iycA00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4iycB00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4iycC00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

Domain ID domain_id	4iycD00
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	240 — Leukocidin-like
Homologous superfamily homologous superfamily	10 — Leukocidin/porin MspA

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Unit-cell length a length_a	94.480 Å
Unit-cell length b length_b	94.480 Å
Unit-cell length c length_c	310.370 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	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	46.700 Å
R factor r_factor	0.1977
R_work r_work	0.1951
R_free r_free	0.2458

Description description	LukS-PV
Molecular weight formula_weight	33110.4 kDa
Mutation mutation	T244A
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9119

Structure of the T244A mutant of the PANTON-VALENTINE LEUCOCIDIN component from STAPHYLOCOCCUS AUREUS

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

LukS-PV

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

4iyc__assembly_2__model_1

4iyc__assembly_2__model_1 | I(q)

4iyc__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (4)

Source organism organism	Staphylococcus phage PVL
NCBI taxonomy ID ncbi_taxonomy_id	71366
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	319

Structure of the T244A mutant of the PANTON-VALENTINE LEUCOCIDIN component from STAPHYLOCOCCUS AUREUS

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

LukS-PV

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

4iyc__assembly_2__model_1

4iyc__assembly_2__model_1 | I(q)

4iyc__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (4)