SAXSdb — 1gzf

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

MONO-ADP-RIBOSYLTRANSFERASE C3

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	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SULFATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARC3_CBDP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 41–251 Author chain B； PDBConstruct 1–211； UniProt 41–251 Author chain C； PDBConstruct 1–211； UniProt 41–251 Author chain D； PDBConstruct 1–211； UniProt 41–251

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	1gzf
Deposition date deposition_date	2002-05-21
Structure title title	Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD
Keywords keywords	TRANSFERASE, ADP-RIBOSYLTRANSFERASE, BACTERIAL TOXIN, C3 EXOENZYME; TRANSFERASE
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.

1gzf__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1gzf__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1gzf__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	17.88 Å
Rg (electron density)	16.97 Å
Total Rg	18.01 Å
Atom count	1679
Residues	208
Excluded volume	29976 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1gzf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1gzf__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1gzf__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1gzf__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 (6)

Entity 1 Entity 1 polymer

Description description	MONO-ADP-RIBOSYLTRANSFERASE C3
Molecular weight formula_weight	23592.0 kDa
EC 编号 ec_number	2.4.2.-
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	7223

AYSNTYQEFTNIDQAKAWGNAQYKKYGLSKSEKEAIVSYTKSASEINGKLRQNKGVINGFPSNLIKQVELLDKSFNKMKTPENIMLFRGDDPAYLGTEFQNTLLNSNGTINKTAFEKAKAKFLNKDRLEYGYISTSLMNVSQFAGRPIITKFKVAKGSKAGYIDPISAFAGQLEMLLPRHSTYHIDDMRLSSDGKQIIITATMMGTAINPK

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	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	3-(AMINOCARBONYL)-1-[(3R,4S,5R)-3,4-DIHYDROXY-5-METHYLTETRAHYDRO-2-FURANYL]PYRIDINIUM
Molecular weight formula_weight	242.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	570

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1gzfa_
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.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d1gzfb_
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.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d1gzfc_
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.166.1.1 — ADP-ribosylating toxins

Domain ID domain_id	d1gzfd_
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.166.1.1 — ADP-ribosylating toxins

CATH v4.4 (4 domains)

Domain ID domain_id	1gzfA00
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	1gzfB00
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	1gzfC00
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	1gzfD00
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	103.947 Å
Unit-cell length b length_b	74.191 Å
Unit-cell length c length_c	119.680 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.10 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2770

Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD

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

MONO-ADP-RIBOSYLTRANSFERASE C3

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

1gzf__assembly_3__model_1

1gzf__assembly_3__model_1 | I(q)

1gzf__assembly_3__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the Clostridium botulinum C3 exoenzyme (wild-type) in complex with NAD

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

MONO-ADP-RIBOSYLTRANSFERASE C3

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

1gzf__assembly_3__model_1

1gzf__assembly_3__model_1 | I(q)

1gzf__assembly_3__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)