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9vyl

Crystal structure of BdThsB1 with NAD

Method: X-RAY DIFFRACTION D_max: 180.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vyl
deposition_date	2025-07-21
last_revision	2026-01-28
title	Crystal structure of BdThsB1 with NAD
keywords	immune recognition, sensor, anti phage, NAD cyclase, TIR domain, Thoeris, Cytobacillus dafuensis, zinc finger, IMMUNE SYSTEM; IMMUNE SYSTEM
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	46.39 Å
rg_electron	47.58 Å
i0	179194000.00
molecular_weight	108410.0 kDa
excluded_volume	135030 Å³
envelope_volume	193230 Å³
shell_volume	39870 Å³
envelope_diameter	177.5 Å
shell_rg	41.72 Å
envelope_rg	47.19 Å
shape_rg	47.61 Å
total_rg	47.19 Å
total_atoms	7612
n_residues	892
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	180.4 Å
rg_real	47.41 Å
rg_real_error	2.77 Å
i0_real	1.7920e+08
i0_real_error	3.7800e+06
rg_reciprocal	46.40 Å
i0_reciprocal	179000000.0000
total_estimate	0.7028
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	31.8 Å
skewness	0.672
kurtosis	-0.206
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	10350000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.327; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.290; Smooth: 0.861

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Putative cyclic ADP-D-ribose synthase TIR1
formula_weight	28443.5 kDa
ec_number	3.2.2.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8622

MKSSHHHHHHENLYFQSNAMGRKIFISYKYSDSGVYPLNGNYSTTVRDYVDELQSKLKEGDHINKGEADGEDLSEFKDETIWTKLKDKIFDSSITIIFISKNMKALFQSEEDQWIPWEISYSLRELTRNGRTSGANALLAVVLPDQYNSYEYFIHDNSCPYCNCITLKTNTLFTILRENMFNIKSPTYNDCSNHSESNKVYTGESSYVRSVKWVDFIDNFDIYLQVAYNINENKDEYTLHKSV

Source

organism	Cytobacillus dafuensis
ncbi_taxonomy_id	1742359
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	SPERMIDINE
formula_weight	145.2 kDa
src_method	nat
entity_count	8

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	24

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1010

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6. Citations (1)

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length_a	43.586 Å
length_b	43.574 Å
length_c	285.783 Å
angle_alpha	90.00 °
angle_beta	90.03 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.539 Å
resolution_low	34.668 Å
r_factor	—
r_work	0.1472
r_free	0.1828

fit	/app/data/saxs_computation/vy/9vyl/9vyl.fit
pddf	/app/data/pr_computation/vy/9vyl/9vyl.pr.out
profile	/app/data/saxs_computation/vy/9vyl/9vyl.dat