SAXSdb — 5umi

▼

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 5	PA50 Fab Light chain × 2 PA50 Fab Heavy chain × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TOXA_CLODI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 22–271； UniProt 2461–2710

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5umi
Deposition date deposition_date	2017-01-27
Structure title title	Clostridium difficile TcdA-CROPs bound to PA50 Fab
Keywords keywords	toxin antibody, TOXIN-IMMUNE SYSTEM complex; TOXIN/IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5umi__assembly_1__model_1

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

Download this curve (.dat)

5umi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5umi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.40 Å
Rg (electron density)	37.05 Å
Total Rg	37.56 Å
Atom count	13425
Residues	886
Excluded volume	121060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5umi__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Toxin A
Molecular weight formula_weight	30318.7 kDa
EC 编号 ec_number	3.4.22.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	13425

MGSSHHHHHHSSGLVPRGSHMGLRTIDGKKYYFNTNTAVAVTGWQTINGKKYYFNTNTSIASTGYTIISGKHFYFNTDGIMQIGVFKGPDGFEYFAPANTDANNIEGQAIRYQNRFLYLHDNIYYFGNNSKAATGWVTIDGNRYYFEPNTAMGANGYKTIDNKNFYFRNGLPQIGVFKGSNGFEYFAPANTDANNIEGQAIRYQNRFLHLLGKIYYFGNNSKAVTGWQTINGKVYYFMPDTAMAAAGGLFEIDGVIYFFGVDGVKAPGIYG

Source Source

Source organism organism	Clostridioides difficile
NCBI taxonomy ID ncbi_taxonomy_id	1496
Host organism host_organism	Bacillus megaterium

Entity 2 Entity 2 polymer

Description description	PA50 Fab Light chain
Molecular weight formula_weight	22999.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EIVLTQSPATLSLSPGERATLSCRASSSVNYMNWYQQKPGQAPRPLIYATSNLASGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQWSSRTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	PA50 Fab Heavy chain
Molecular weight formula_weight	23826.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,A

QVQLVQSGAEVKKPGASVKVSCKASGYTFTDYNMDWVRQAPGQRLEWMGDINPKYDIIGHNPKFMGRVTITRDTSASTAYMELSSLRSEDTAVYYCARSDRGWYFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

▼

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

Domain ID domain_id	5umiB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5umiC01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	270 — left handed beta-beta-3-solenoid
Homologous superfamily homologous superfamily	10 — Cholin Binding

Domain ID domain_id	5umiC02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	270 — left handed beta-beta-3-solenoid
Homologous superfamily homologous superfamily	10 — Cholin Binding

Domain ID domain_id	5umiC03
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	270 — left handed beta-beta-3-solenoid
Homologous superfamily homologous superfamily	10 — Cholin Binding

Domain ID domain_id	5umiH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5umiL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5umiL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

Unit-cell length a length_a	93.685 Å
Unit-cell length b length_b	77.330 Å
Unit-cell length c length_c	97.781 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	3.230 Å
Low-resolution limit resolution_low	48.884 Å
R factor r_factor	0.2710
R_work r_work	0.2700
R_free r_free	0.2896

Clostridium difficile TcdA-CROPs bound to PA50 Fab

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

5umi__assembly_1__model_1

5umi__assembly_1__model_1 | I(q)

5umi__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 (3)

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

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)

Clostridium difficile TcdA-CROPs bound to PA50 Fab

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

5umi__assembly_1__model_1

5umi__assembly_1__model_1 | I(q)

5umi__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 (3)

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

6. Fold Classification (SCOP + CATH) 7 domains

CATH v4.4 (7 domains)

7. Citations (1)