2j3z

Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 6.1

Method: X-RAY DIFFRACTION

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

C2 TOXIN COMPONENT I

CLOSTRIDIUM BOTULINUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 GLYCEROL × 4 SULFATE ION × 5 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 2 GLYCEROL × 2 SULFATE ION × 8 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 GLYCEROL × 2 SULFATE ION × 7 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 GLYCEROL × 2 SULFATE ION × 6 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 GLYCEROL × 1 SULFATE ION × 7 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 GLYCEROL × 1 SULFATE ION × 7 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O69275_CLOBO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–431； UniProt 1–431 Author chain B； PDBConstruct 1–431； UniProt 1–431 Author chain C； PDBConstruct 1–431； UniProt 1–431 Author chain D； PDBConstruct 1–431； UniProt 1–431 Author chain E； PDBConstruct 1–431； UniProt 1–431 Author chain F； PDBConstruct 1–431； UniProt 1–431

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	2j3z
Deposition date deposition_date	2006-08-23
Structure title title	Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 6.1
Keywords keywords	ADP-RIBOSYLTRANSFERASE, TOXIN, CLOSTRIDIUM BOTULINUM; 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.

2j3z__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2j3z__assembly_6__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2j3z__assembly_6__model_1 | P(r) · Pending

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

Rg（Guinier）	25.02 Å
Rg (electron density)	23.81 Å
Total Rg	24.74 Å
Atom count	3443
Residues	421
Excluded volume	61272 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2j3z__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2j3z__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2j3z__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2j3z__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2j3z__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2j3z__assembly_6__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 (5)

Entity 1 Entity 1 polymer

Description description	C2 TOXIN COMPONENT I
Molecular weight formula_weight	49391.7 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	21502

MPIIKEPIDFINKPESEAKKWGKEEEKRWFTKLNNLEEVAVNQLKNKEYKTKIDNFSTDILFSSLTAIEIMKEDENRNLFDVERIREALLKNTLDRDAIGYVNFTPKELGINFSIRDVELDRDISDETLDKVRQQIINQEYTKFSFISLGLNDNSINESVPVIVKTRVPTTFDYGVLNDKETVSLLLNQGFSIIPESAIITTIKGKDYILIEGSLSQELDFYNKGSEAWGAENYGDYISKLSHEQLGALEGYLHSDYKAINSYLRNNRVPNNDELNKKIELISSALSVKPIPQTLIAYRRVDGIPFDLPSDFSFDKKENGEIIADKQKLNEFIDKWTGKEIENLSFSSTSLKSTPSSFSKSRFIFRLRLSEGAIGAFIYGFSGFQDEQEILLNKNSTFKIFRITPITSIINRVTKMTQVVIDAEGIQNKEI

Source Source

Source organism organism	CLOSTRIDIUM BOTULINUM
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	40

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	592

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6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d2j3za1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3za2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3ze1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

Domain ID domain_id	d2j3zf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.166 — ADP-ribosylation
Superfamily Superfamily superfamily	d.166.1 — ADP-ribosylation
Family Family family	d.166.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	2j3zA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zC02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zD02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zE01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zE02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zF01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

Domain ID domain_id	2j3zF02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

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Unit-cell length a length_a	93.421 Å
Unit-cell length b length_b	272.898 Å
Unit-cell length c length_c	246.290 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2010
R_work r_work	0.2000
R_free r_free	0.2580

Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 6.1

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

C2 TOXIN COMPONENT I

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

2j3z__assembly_6__model_1

2j3z__assembly_6__model_1 | I(q)

2j3z__assembly_6__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (11 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the enzymatic component C2-I of the C2-toxin from Clostridium botulinum at pH 6.1

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

C2 TOXIN COMPONENT I

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

2j3z__assembly_6__model_1

2j3z__assembly_6__model_1 | I(q)

2j3z__assembly_6__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (11 domains)

CATH v4.4 (12 domains)

7. Citations (1)