SAXSdb — 9bbf

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

ADP-ribosyltransferase binding component

Clostridioides difficile

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	ADP-ribosyltransferase enzymatic component × 1 （Q9KH42） CALCIUM ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8DS70_CLODI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–835； UniProt 43–876 Author chain B； PDBConstruct 2–835； UniProt 43–876 Author chain C； PDBConstruct 2–835； UniProt 43–876 Author chain D； PDBConstruct 2–835； UniProt 43–876 Author chain E； PDBConstruct 2–835； UniProt 43–876 Author chain F； PDBConstruct 2–835； UniProt 43–876 Author chain G； PDBConstruct 2–835； UniProt 43–876

ADP-ribosyltransferase enzymatic component

Clostridioides difficile

UniProt Q9KH42

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	ADP-ribosyltransferase binding component × 7 （A8DS70） CALCIUM ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9KH42_CLODI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Z； PDBConstruct 1–414； UniProt 50–463

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	9bbf
Deposition date deposition_date	2024-04-05
Structure title title	Structure of Clostridioides difficile Component A (50-463) in Complex with a CDTb Oligomer
Keywords keywords	Clostridioides, difficile, toxin, CDT, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

9bbf__assembly_1__model_1

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

Download this curve (.dat)

9bbf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bbf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.10 Å
Rg (electron density)	40.63 Å
Total Rg	41.19 Å
Atom count	19880
Residues	2533
Excluded volume	353130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bbf__assembly_1__model_1`	octameric （8）	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 (3)

Entity 1 Entity 1 polymer

Description description	ADP-ribosyltransferase binding component
Molecular weight formula_weight	94289.4 kDa
Source method src_method	man
Copy count entity_count	7

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G
Atom count atom_count	19880

MEIVNEDILPNNGLMGYYFTDEHFKDLKLMAPIKDGNLKFEEKKVDKLLDKDKSDVKSIRWTGRIIPSKDGEYTLSTDRDDVLMQVNTESTISNTLKVNMKKGKEYKVRIELQDKNLGSIDNLSSPNLYWELDGMKKIIPEENLFLRDYSNIEKDDPFIPNNNFFDPKLMSDWEDEDLDTDNDNIPDSYERNGYTIKDLIAVKWEDSFAEQGYKKYVSNYLESNTAGDPYTDYEKASGSFDKAIKTEARDPLVAAYPIVGVGMEKLIISTNEHASTDQGKTVSRATTNSKTESNTAGVSVNVGYQNGFTANVTTNYSHTTDNSTAVQDSNGESWNTGLSINKGESAYINANVRYYNTGTAPMYKVTPTTNLVLDGDTLSTIKAQENQIGNNLSPGDTYPKKGLSPLALNTMDQFSSRLIPINYDQLKKLDAGKQIKLETTQVSGNFGTKNSSGQIVTEGNSWSDYISQIDSISASIILDTENESYERRVTAKNLQDPEDKTPELTIGEAIEKAFGATKKDGLLYFNDIPIDESCVELIFDDNTANKIKDSLKTLSDKKIYNVKLERGMNILIKTPTYFTNFDDYNNYPSTWSNVNTTNQDGLQGSANKLNGETKIKIPMSELKPYKRYVFSGYSKDPLTSNSIIVKIKAKEEKTDYLVPEQGYTKFSYEFETTEKDSSNIEITLIGSGTTYLDNLSITELNSTPEILDEPEVKIPTDQEIMDAHKIYFADLNFNPSTGNTYINGMYFAPTQTNKEALDYIQKYRVEATLQYSGFKDIGTKDKEMRNYLGDPNQPKTNYVNLRSYFTGGENIMTYKKLRIYAITPDDRELLVLSVD

Source Source

Source organism organism	Clostridioides difficile
NCBI taxonomy ID ncbi_taxonomy_id	1496
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	ADP-ribosyltransferase enzymatic component
Molecular weight formula_weight	47626.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

KAPIERPEDFLKDKEKAKEWERKEAERIEQKLERSEKEALESYKKDSVEISKYSQTRNYFYDYQIEANSREKEYKELRNAISKNKIDKPMYVYYFESPEKFAFNKVIRTENQNEISLEKFNEFKETIQNKLFKQDGFKDISLYEPGKGDEKPTPLLMHLKLPRNTGMLPYTNTNNVSTLIEQGYSIKIDKIVRIVIDGKHYIKAEASVVSSLDFKDDVSKGDSWGKANYNDWSNKLTPNELADVNDYMRGGYTAINNYLISNGPVNNPNPELDSKITNIENALKREPIPTNLTVYRRSGPQEFGLTLTSPEYDFNKLENIDAFKSKWEGQALSYPNFISTSIGSVNMSAFAKRKIVLRITIPKGSPGAYLSAIPGYAGEYEVLLNHGSKFKINKIDSYKDGTITKLIVDATLIP

Source Source

Source organism organism	Clostridioides difficile
NCBI taxonomy ID ncbi_taxonomy_id	1496
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	14

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	43726

Structure of Clostridioides difficile Component A (50-463) in Complex with a CDTb Oligomer

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

ADP-ribosyltransferase binding component

State in the Current Structure

Other States of the Same Protein in the Database

ADP-ribosyltransferase enzymatic component

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

9bbf__assembly_1__model_1

9bbf__assembly_1__model_1 | I(q)

9bbf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 non-polymer

7. Citations (1)

Structure of Clostridioides difficile Component A (50-463) in Complex with a CDTb Oligomer

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

ADP-ribosyltransferase binding component

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ADP-ribosyltransferase enzymatic component

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

9bbf__assembly_1__model_1

9bbf__assembly_1__model_1 | I(q)

9bbf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 non-polymer

7. Citations (1)