3m2l

Crystal structure of the M113F mutant of alpha-hemolysin

Method: X-RAY DIFFRACTION

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

Alpha-hemolysin

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 7	water × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HLA_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–294； UniProt 27–319 Author chain B； PDBConstruct 2–294； UniProt 27–319 Author chain C； PDBConstruct 2–294； UniProt 27–319 Author chain D； PDBConstruct 2–294； UniProt 27–319 Author chain E； PDBConstruct 2–294； UniProt 27–319 Author chain F； PDBConstruct 2–294； UniProt 27–319 Author chain G； PDBConstruct 2–294； UniProt 27–319

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	3m2l
Deposition date deposition_date	2010-03-07
Structure title title	Crystal structure of the M113F mutant of alpha-hemolysin
Keywords keywords	beta barrel, pore-forming toxin, Cytolysis, Hemolysis, Secreted, 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.

3m2l__assembly_1__model_1

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

Download this curve (.dat)

3m2l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3m2l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.75 Å
Rg (electron density)	38.45 Å
Total Rg	39.09 Å
Atom count	16431
Residues	2051
Excluded volume	289290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3m2l__assembly_1__model_1`	heptameric （7）	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) 14 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d3m2la_
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.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d3m2lb_
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.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d3m2lc_
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.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d3m2ld_
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.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d3m2le_
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.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d3m2lf_
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.6.1.1 — Leukocidin (pore-forming toxin)

Domain ID domain_id	d3m2lg_
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.6.1.1 — Leukocidin (pore-forming toxin)

CATH v4.4 (7 domains)

Domain ID domain_id	3m2lA00
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	3m2lB00
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	3m2lC00
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	3m2lD00
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	3m2lE00
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	3m2lF00
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	3m2lG00
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	151.190 Å
Unit-cell length b length_b	134.800 Å
Unit-cell length c length_c	132.890 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	28

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2410
R_free r_free	0.2750

Description description	Alpha-hemolysin
Molecular weight formula_weight	33437.2 kDa
Mutation mutation	M113F
Source method src_method	man
Copy count entity_count	7

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	16733

Crystal structure of the M113F mutant of alpha-hemolysin

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

Alpha-hemolysin

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

3m2l__assembly_1__model_1

3m2l__assembly_1__model_1 | I(q)

3m2l__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Staphylococcus aureus

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	302

Crystal structure of the M113F mutant of alpha-hemolysin

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

Alpha-hemolysin

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

3m2l__assembly_1__model_1

3m2l__assembly_1__model_1 | I(q)

3m2l__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (7 domains)

CATH v4.4 (7 domains)

7. Citations (1)