SAXSdb — 2f2f

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

Cytolethal distending toxin A

Aggregatibacter actinomycetemcomitans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Cytolethal distending toxin B × 1 （Q7DK12） cytolethal distending toxin C × 1 （Q7DK11） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Cytolethal distending toxin B × 1 （Q7DK12） cytolethal distending toxin C × 1 （Q7DK11） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDTA_ACTAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–222； UniProt 1–222 Author chain D； PDBConstruct 1–222； UniProt 1–222

Cytolethal distending toxin B

Aggregatibacter actinomycetemcomitans

UniProt Q7DK12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Cytolethal distending toxin A × 1 （O87120） cytolethal distending toxin C × 1 （Q7DK11） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Cytolethal distending toxin A × 1 （O87120） cytolethal distending toxin C × 1 （Q7DK11） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7DK12_ACTAC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–283； UniProt 1–283 Author chain E； PDBConstruct 1–283； UniProt 1–283

cytolethal distending toxin C

Aggregatibacter actinomycetemcomitans

UniProt Q7DK11

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Cytolethal distending toxin A × 1 （O87120） Cytolethal distending toxin B × 1 （Q7DK12） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Cytolethal distending toxin A × 1 （O87120） Cytolethal distending toxin B × 1 （Q7DK12） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7DK11_ACTAC
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–186； UniProt 1–186 Author chain F； PDBConstruct 1–186； UniProt 1–186

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	2f2f
Deposition date deposition_date	2005-11-16
Structure title title	Crystal structure of cytolethal distending toxin (CDT) from Actinobacillus actinomycetemcomitans
Keywords keywords	Cytolethal distending toxin, CDT, Actinobacillus actinomycetemcomitans, oligomerization, stability and toxic activity, 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.

2f2f__assembly_1__model_1

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

Download this curve (.dat)

2f2f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f2f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.69 Å
Rg (electron density)	23.61 Å
Total Rg	24.43 Å
Atom count	4458
Residues	568
Excluded volume	78814 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f2f__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2f2f__assembly_2__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Cytolethal distending toxin A
Molecular weight formula_weight	24532.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	9188

MKKFLPGLLLMGLVACSSNQRMSDYSQPESQSDLAPKSSTTQFQPQPLLSKASSMPLNLLSSSKNGQVSPSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKIEPGKHREYFRFVNQSLGTCIEAYGNGLIHDTCSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSPTYYSTVTLSTCDGATEPLRDQTWYLAPPVLEATAVN

Source Source

Source organism organism	Aggregatibacter actinomycetemcomitans
NCBI taxonomy ID ncbi_taxonomy_id	714
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cytolethal distending toxin B
Molecular weight formula_weight	31528.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MQWVKQLNVVFCTMLFSFSSYANLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFTSSPSSPERRGYSWMVVGDFNRAPVNLEAALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVHDR

Source Source

Source organism organism	Aggregatibacter actinomycetemcomitans
NCBI taxonomy ID ncbi_taxonomy_id	714
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	cytolethal distending toxin C
Molecular weight formula_weight	20731.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MKKYLLSFLLSMILTLTSHAESNPDPTTYPDVELSPPPRISLRSLLTAQPIKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFPGEGTTDCKDIDHTVFNLIPTNTGAFLIKDALLGFCMTSHDFDDLRLEPCGISVSGRTFSLAYQWGILPPFGPSKILRPPVGRNQGS

Source Source

Source organism organism	Aggregatibacter actinomycetemcomitans
NCBI taxonomy ID ncbi_taxonomy_id	714
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	272

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2f2fa1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d2f2fb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.151 — DNase I-like
Superfamily Superfamily superfamily	d.151.1 — DNase I-like
Family Family family	d.151.1.1 — DNase I-like

Domain ID domain_id	d2f2fc1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d2f2fd_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d2f2fe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.151 — DNase I-like
Superfamily Superfamily superfamily	d.151.1 — DNase I-like
Family Family family	d.151.1.1 — DNase I-like

Domain ID domain_id	d2f2ff_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

CATH v4.4 (6 domains)

Domain ID domain_id	2f2fA00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2f2fB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

Domain ID domain_id	2f2fC00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2f2fD00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2f2fE00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

Domain ID domain_id	2f2fF00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	115.650 Å
Unit-cell length b length_b	117.460 Å
Unit-cell length c length_c	123.370 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2240
R_work r_work	0.2210
R_free r_free	0.2510

Crystal structure of cytolethal distending toxin (CDT) from Actinobacillus actinomycetemcomitans

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

Cytolethal distending toxin A

State in the Current Structure

Other States of the Same Protein in the Database

Cytolethal distending toxin B

State in the Current Structure

Other States of the Same Protein in the Database

cytolethal distending toxin C

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

2f2f__assembly_1__model_1

2f2f__assembly_1__model_1 | I(q)

2f2f__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of cytolethal distending toxin (CDT) from Actinobacillus actinomycetemcomitans

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

Cytolethal distending toxin A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cytolethal distending toxin B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

cytolethal distending toxin C

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

2f2f__assembly_1__model_1

2f2f__assembly_1__model_1 | I(q)

2f2f__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)