SAXSdb — 1kho

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

alpha-toxin

Clostridium perfringens

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHLC2_CLOPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–370； UniProt 29–398 Author chain B； PDBConstruct 1–370； UniProt 29–398

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	1kho
Deposition date deposition_date	2001-11-30
Structure title title	Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP
Keywords keywords	N-terminal alpha-helix, C-terminal beta-sheet, 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.

1kho__assembly_1__model_1

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

Download this curve (.dat)

1kho__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kho__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.09 Å
Rg (electron density)	21.22 Å
Total Rg	22.07 Å
Atom count	2998
Residues	370
Excluded volume	52412 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kho__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1kho__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	alpha-toxin
Molecular weight formula_weight	42421.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6148

WDGKADGTGTHAMIATQGVTILENDLSSNEPEVIRNNLEILKQNMHDLQLGSTYPDYDKNAYDLYQDHFWDPDTDNNFTKDSKWYLSYSIPDTAESQIRKFSALARYEWKRGNYKQATFYLGEAMHYFGDADTPYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSKTNDAFYSNILTNEDFNSWSKEFARSFAKTAKDLYYSHANMSCSWDEWDYAAKVALANSQKGTSGYIYRFLHDVSDGKDSSANKNVNELVAYITTGGEKYAGTDDYMYFGIKTKDGQTQEWTMDNPGNDFMTGSQDTYTFKLKDKNLKIDDIQNMWIRKSKYTEFGDDYKPANIKVIANGNVVLNKDINEWISGNSTYNIK

Source Source

Source organism organism	Clostridium perfringens
NCBI taxonomy ID ncbi_taxonomy_id	1502
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	152

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1khoa1
Class class	a — All alpha proteins
Fold Fold fold	a.124 — Phospholipase C/P1 nuclease
Superfamily Superfamily superfamily	a.124.1 — Phospholipase C/P1 nuclease
Family Family family	a.124.1.1 — Phospholipase C

Domain ID domain_id	d1khoa2
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.3 — Alpha-toxin, C-terminal domain

Domain ID domain_id	d1khob1
Class class	a — All alpha proteins
Fold Fold fold	a.124 — Phospholipase C/P1 nuclease
Superfamily Superfamily superfamily	a.124.1 — Phospholipase C/P1 nuclease
Family Family family	a.124.1.1 — Phospholipase C

Domain ID domain_id	d1khob2
Class class	b — All beta proteins
Fold Fold fold	b.12 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Superfamily Superfamily superfamily	b.12.1 — Lipase/lipooxygenase domain (PLAT/LH2 domain)
Family Family family	b.12.1.3 — Alpha-toxin, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1khoA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	575 — P1 Nuclease
Homologous superfamily homologous superfamily	10 — P1 Nuclease

Domain ID domain_id	1khoA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

Domain ID domain_id	1khoB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	575 — P1 Nuclease
Homologous superfamily homologous superfamily	10 — P1 Nuclease

Domain ID domain_id	1khoB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	60 — Lipoxygenase-1
Homologous superfamily homologous superfamily	20 — PLAT/LH2 domain

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Unit-cell length a length_a	117.230 Å
Unit-cell length b length_b	117.230 Å
Unit-cell length c length_c	220.590 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	16

Space group space_group	P 41 2 2
Space-group number int_tables_number	91
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2098
R_free r_free	0.2361

Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP

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

alpha-toxin

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

1kho__assembly_1__model_1

1kho__assembly_1__model_1 | I(q)

1kho__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure Analysis of Clostridium perfringens alpha-Toxin Isolated from Avian Strain SWCP

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

alpha-toxin

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

1kho__assembly_1__model_1

1kho__assembly_1__model_1 | I(q)

1kho__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)