SAXSdb — 8yvo

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

Toxin A

Clostridioides difficile

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	C4.2 nanobody × 1 1,2-ETHANEDIOL × 5 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	C4.2 nanobody × 1 1,2-ETHANEDIOL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TCDA_CLODI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–69； UniProt 2639–2707 Author chain D； PDBConstruct 1–69； UniProt 2639–2707

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	8yvo
Deposition date deposition_date	2024-03-28
Last revision last_revision	2024-12-18
Structure title title	Crystal structure of the C. difficile toxin A CROPs domain fragment 2639-2707 bound to C4.2 nanobody
Keywords keywords	CROPs domain fragment, Toxin A, Complex with nanobody, Clostridioides difficile, TOXIN, TOXIN-IMMUNE SYSTEM complex; TOXIN/IMMUNE SYSTEM
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.

8yvo__assembly_1__model_1

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

Download this curve (.dat)

8yvo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yvo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.17 Å
Rg (electron density)	18.78 Å
Total Rg	19.73 Å
Atom count	1525
Residues	196
Excluded volume	27027 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yvo__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8yvo__assembly_2__model_1`	dimeric （2）	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	C4.2 nanobody
Molecular weight formula_weight	18550.7 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	3428

MKYLLPTAAAGLLLLAAQPAMAEVQLVESGGGSVQAGGSLRLSCAASAFGNYMGWFRQAPGKEREGVAAIRTGGGSTYYTDSVKGRFTISQDKAKNTVYLQMNSLKPEDTAMYVCATAGDRWHATDAFILRDFVYEYWGQGTQVTVSSAAAEQKLISEEDLNGAAHHHHHHGS

Source Source

Source organism organism	Camelus dromedarius
NCBI taxonomy ID ncbi_taxonomy_id	9838
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Toxin A
Molecular weight formula_weight	7685.8 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

AIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAMG

Source Source

Source organism organism	Clostridioides difficile
NCBI taxonomy ID ncbi_taxonomy_id	1496
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	350

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Unit-cell length a length_a	113.804 Å
Unit-cell length b length_b	42.850 Å
Unit-cell length c length_c	178.277 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.11 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.420 Å
R factor r_factor	0.2113
R_work r_work	0.2099
R_free r_free	0.2384

Crystal structure of the C. difficile toxin A CROPs domain fragment 2639-2707 bound to C4.2 nanobody

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

Toxin A

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

8yvo__assembly_1__model_1

8yvo__assembly_1__model_1 | I(q)

8yvo__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 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of the C. difficile toxin A CROPs domain fragment 2639-2707 bound to C4.2 nanobody

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8yvo__assembly_1__model_1

8yvo__assembly_1__model_1 | I(q)

8yvo__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 non-polymer

Entity 4 Entity 4 water

7. Citations (1)