1m3i

Perfringolysin O, new crystal form

Method: X-RAY DIFFRACTION

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

perfringolysin O

Clostridium perfringens

UniProt P19995

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	TACY_CLOPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 30–500 Author chain B； PDBConstruct 1–471； UniProt 30–500 Author chain C； PDBConstruct 1–471； UniProt 30–500 Author chain D； PDBConstruct 1–471； UniProt 30–500

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	1m3i
Deposition date deposition_date	2002-06-28
Structure title title	Perfringolysin O, new crystal form
Keywords keywords	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.

1m3i__assembly_2__model_1

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

Download this curve (.dat)

1m3i__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m3i__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	32.54 Å
Rg (electron density)	33.07 Å
Total Rg	33.00 Å
Atom count	3657
Residues	465
Excluded volume	64867 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m3i__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m3i__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1m3i__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1m3i__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)

Entity 1 Entity 1 polymer

Description description	perfringolysin O
Molecular weight formula_weight	52571.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	14920

DITDKNQSIDSGISSLSYNRNEVLASNGDKIESFVPKEGKKAGNKFIVVERQKRSLTTSPVDISIIDSVNDRTYPGALQLADKALVENRPTILMVKRKPININIDLPGLKGENSIKVDDPTYGKVSGAIDELVSKWNEKYSSTHTLPARTQYSESMVYSKSQISSALNVNAKVLENSLGVDFNAVANNEKKVMILAYKQIFYTVSADLPKNPSDLFDDSVTFNDLKQKGVSNEAPPLMVSNVAYGRTIYVKLETTSSSKDVQAAFKALIKNTDIKNSQQYKDIYENSSFTAVVLGGDAQEHNKVVTKDFDEIRKVIKDNATFSTKNPAYPISYTSVFLKDNSVAAVHNKTDYIETTSTEYSKGKINLDHSGAYVAQFEVAWDEVSYDKEGNEVLTHKTWDGNYQDKTAHYSTVIPLEANARNIRIKARECTGLAWEWWRDVISEYDVPLTNNINVSIWGTTLYPGSSITYN

Source Source

Source organism organism	Clostridium perfringens
NCBI taxonomy ID ncbi_taxonomy_id	1502
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	292

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1m3ia1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d1m3ia2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

Domain ID domain_id	d1m3ib1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d1m3ib2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

Domain ID domain_id	d1m3ic1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d1m3ic2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

Domain ID domain_id	d1m3id1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.69 — Perfringolysin N-terminal-like
Superfamily Superfamily superfamily	f.69.1 — Perfringolysin N-terminal-like
Family Family family	f.69.1.1 — Perfringolysin N-terminal-like

Domain ID domain_id	d1m3id2
Class class	b — All beta proteins
Fold Fold fold	b.183 — Perfringolysin C-terminal-like
Superfamily Superfamily superfamily	b.183.1 — Perfringolysin C-terminal-like
Family Family family	b.183.1.1 — Perfringolysin C-terminal-like

CATH v4.4 (16 domains)

Domain ID domain_id	1m3iA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	1m3iA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1m3iA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	1m3iA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	1m3iB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	1m3iB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1m3iB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	1m3iB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	1m3iC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	1m3iC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1m3iC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	1m3iC04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

Domain ID domain_id	1m3iD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	840 — HIV-1 Reverse Transcriptase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain

Domain ID domain_id	1m3iD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1m3iD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	40 — Perfringolysin

Domain ID domain_id	1m3iD04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1430 — Perfringolysin, domain 4

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Unit-cell length a length_a	130.410 Å
Unit-cell length b length_b	130.410 Å
Unit-cell length c length_c	129.900 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	12

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2330
R_free r_free	0.2800

Perfringolysin O, new crystal form

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

perfringolysin O

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

1m3i__assembly_2__model_1

1m3i__assembly_2__model_1 | I(q)

1m3i__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) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Perfringolysin O, new crystal form

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

perfringolysin O

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

1m3i__assembly_2__model_1

1m3i__assembly_2__model_1 | I(q)

1m3i__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) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (1)