SAXSdb — 1sr4

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

Cytolethal distending toxin subunit A

Haemophilus ducreyi

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 protein B × 1 （O06523） cytolethal distending toxin protein C × 1 （O06524） BROMIDE ION × 26 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDTA_HAEDU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–206； UniProt 18–223

cytolethal distending toxin protein B

Haemophilus ducreyi

UniProt O06523

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 subunit A × 1 （O06522） cytolethal distending toxin protein C × 1 （O06524） BROMIDE ION × 26 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O06523_HAEDU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–261； UniProt 23–283

cytolethal distending toxin protein C

Haemophilus ducreyi

UniProt O06524

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 subunit A × 1 （O06522） cytolethal distending toxin protein B × 1 （O06523） BROMIDE ION × 26 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O06524_HAEDU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–166； UniProt 21–186

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	1sr4
Deposition date deposition_date	2004-03-22
Structure title title	Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin
Keywords keywords	;toxin, bacterial, Haemophilus ducreyi, virulence, DNA Damage, genotoxin, cytotoxins, Cell Cycle, Apoptosis, lectin, Deoxyribonuclease I ;; 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.

1sr4__assembly_1__model_1

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

Download this curve (.dat)

1sr4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1sr4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.14 Å
Rg (electron density)	23.92 Å
Total Rg	24.96 Å
Atom count	4562
Residues	579
Excluded volume	81006 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1sr4__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Cytolethal distending toxin subunit A
Molecular weight formula_weight	22873.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5039

SNQRMNDYSQPESQSDLAPKSSTIQPQPQPLLSKTPSMSLNLLSSSGPNRQVLPSEPSNFMTLMGQNGALLTVWALAKRNWLWAYPNIYSQDFGNIRNWKMEPGKHREYFRFVNQSLGTCVEAYGNGLIHDICSLDKLAQEFELLPTDSGAVVIKSVSQGRCVTYNPVSTTFYSTVTLSVCDGATEPSRDQTWYLAPPVLEATAVN

Source Source

Source organism organism	Haemophilus ducreyi
NCBI taxonomy ID ncbi_taxonomy_id	730
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	cytolethal distending toxin protein B
Molecular weight formula_weight	28989.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

NLSDFKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRPAVGIRIGTDVFFTVHALATGGSDAVSLIRNIFTTFNSSSSPPERRVYSWMVVGDFNRAPANLEVALRQEPAVSENTIIIAPTEPTHRSGNILDYAILHDAHLPRREQARERIGASLMLNQLRSQITSDHFPVSFVRDR

Source Source

Source organism organism	Haemophilus ducreyi
NCBI taxonomy ID ncbi_taxonomy_id	730
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	cytolethal distending toxin protein C
Molecular weight formula_weight	18379.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ESNPDPTTYPDVELSPPPRISLRSLLTAQPVKNDHYDSHNYLSTHWELIDYKGKEYEKLRDGGTLVQFKVVGAAKCFAFLGKGTTDCKDTDHTVFNLIPTNTGAFLIKDALLGFCITSHDFDDLKLEPCGGSVSGRTFSLAYQWGILPPFGPSKILIPPVRRNQGS

Source Source

Source organism organism	Haemophilus ducreyi
NCBI taxonomy ID ncbi_taxonomy_id	730
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	26

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	477

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1sr4a_
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	d1sr4b_
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	d1sr4c_
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 (3 domains)

Domain ID domain_id	1sr4A00
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	1sr4B00
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	1sr4C00
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	71.652 Å
Unit-cell length b length_b	75.653 Å
Unit-cell length c length_c	121.637 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	4

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

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	99.000 Å
R factor r_factor	0.1820
R_work r_work	0.1820
R_free r_free	0.2140

Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin

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

Cytolethal distending toxin subunit A

State in the Current Structure

Other States of the Same Protein in the Database

cytolethal distending toxin protein B

State in the Current Structure

Other States of the Same Protein in the Database

cytolethal distending toxin protein 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

1sr4__assembly_1__model_1

1sr4__assembly_1__model_1 | I(q)

1sr4__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin

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

Cytolethal distending toxin subunit 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 protein 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 protein 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

1sr4__assembly_1__model_1

1sr4__assembly_1__model_1 | I(q)

1sr4__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)