SAXSdb — 9vyl

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

Putative cyclic ADP-D-ribose synthase TIR1

Cytobacillus dafuensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 SPERMIDINE × 8 ZINC ION × 4 SODIUM ION × 24 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THSB1_CYTDA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–243； UniProt 1–224 Author chain B； PDBConstruct 20–243； UniProt 1–224 Author chain C； PDBConstruct 20–243； UniProt 1–224 Author chain D； PDBConstruct 20–243； UniProt 1–224

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	9vyl
Deposition date deposition_date	2025-07-21
Last revision last_revision	2026-01-28
Structure title title	Crystal structure of BdThsB1 with NAD
Keywords keywords	immune recognition, sensor, anti phage, NAD cyclase, TIR domain, Thoeris, Cytobacillus dafuensis, zinc finger, IMMUNE SYSTEM; 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.

9vyl__assembly_1__model_1

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

Download this curve (.dat)

9vyl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vyl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.39 Å
Rg (electron density)	47.58 Å
Total Rg	47.19 Å
Atom count	7612
Residues	892
Excluded volume	135030 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vyl__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Putative cyclic ADP-D-ribose synthase TIR1
Molecular weight formula_weight	28443.5 kDa
EC 编号 ec_number	3.2.2.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8622

MKSSHHHHHHENLYFQSNAMGRKIFISYKYSDSGVYPLNGNYSTTVRDYVDELQSKLKEGDHINKGEADGEDLSEFKDETIWTKLKDKIFDSSITIIFISKNMKALFQSEEDQWIPWEISYSLRELTRNGRTSGANALLAVVLPDQYNSYEYFIHDNSCPYCNCITLKTNTLFTILRENMFNIKSPTYNDCSNHSESNKVYTGESSYVRSVKWVDFIDNFDIYLQVAYNINENKDEYTLHKSV

Source Source

Source organism organism	Cytobacillus dafuensis
NCBI taxonomy ID ncbi_taxonomy_id	1742359
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SPERMIDINE
Molecular weight formula_weight	145.2 kDa
Source method src_method	nat
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1010

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Unit-cell length a length_a	43.586 Å
Unit-cell length b length_b	43.574 Å
Unit-cell length c length_c	285.783 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.539 Å
Low-resolution limit resolution_low	34.668 Å
R factor r_factor	—
R_work r_work	0.1472
R_free r_free	0.1828

Crystal structure of BdThsB1 with NAD

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

Putative cyclic ADP-D-ribose synthase TIR1

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

9vyl__assembly_1__model_1

9vyl__assembly_1__model_1 | I(q)

9vyl__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Crystal structure of BdThsB1 with NAD

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

Putative cyclic ADP-D-ribose synthase TIR1

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

9vyl__assembly_1__model_1

9vyl__assembly_1__model_1 | I(q)

9vyl__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)