← Back to search

9yas

Rana catesbeiana saxiphilin mutant - Y558A:STX-C13-OBz (co-crystal)

Method: X-RAY DIFFRACTION D_max: 147.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9yas
deposition_date	2025-09-16
last_revision	2026-05-27
title	Rana catesbeiana saxiphilin mutant - Y558A:STX-C13-OBz (co-crystal)
keywords	Saxiphilin, Toxin resistance, Saxitoxin, ANTITOXIN; ANTITOXIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	44.48 Å
rg_electron	44.16 Å
i0	989364000.00
molecular_weight	168660.0 kDa
excluded_volume	161000 Å³
envelope_volume	326580 Å³
shell_volume	61182 Å³
envelope_diameter	151.2 Å
shell_rg	49.66 Å
envelope_rg	42.95 Å
shape_rg	44.15 Å
total_rg	44.35 Å
total_atoms	12668
n_residues	1636
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

▼

3. P(r) Analysis (GNOM)

dmax	147.8 Å
rg_real	44.47 Å
rg_real_error	1.67 Å
i0_real	9.8940e+08
i0_real_error	1.9880e+07
rg_reciprocal	44.48 Å
i0_reciprocal	989400000.0000
total_estimate	0.6654
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	139.3 Å
skewness	0.257
kurtosis	-0.555
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	28090000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 0.999; Sysdev: 0.010; Positv: 1.000; Valcen: 0.986; Smooth: 0.873

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Saxiphilin
formula_weight	94136.2 kDa
mutation	Y558A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12881

MAPTFQTALFFTIISLSFAAPNAKQVRWCAISDLEQKKCNDLVGSCNVPDITLVCVLRSSTEDCMTAIKDGQADAMFLDSGEVYEASKDPYNLKPIIAEPYSSNRDLQKCLKERQQALAKKMIGHYIPQCDEKGNYQPQQCHGSTGHCWCVNAMGEKISGTNTPPGQTRATCERHELPKCLKERQVALGGDEKVLGRFVPQCDEKGNYEPQQFHGSTGYSWCVNAIGEEIAGTKTPPGKIPATCQKHDLVTTCHYAVAMVKKSSAFQFNQLKGKRSCHSGVSKTDGWKALVTVLVEKKLLSWDGPAKESIQRAMSKFFSVSCIPGATQTNLCKQCKGEEGKNCKNSHDEPYYGNYGAFRCLKEDMGDVAFLRSTALSDEHSEVYELLCPDNTRKPLNKYKECNLGTVPAGTVVTRKISDKTEDINNFLMEAQKRQCKLFSSAHGKDLMFDDSTLQLALLSSEVDAFLYLGVKLFHAMKALTGDAHLPSKNKVRWCTINKLEKMKCDDWSAVSGGAIACTEASCPKGCVKQILKGEADAVKLEVQYMYEALMCGLLPAVEEYHNKDDFGPCKTPGSPATDFGTLRAVALVKKSNKDINWNNIKGKKSCHTGVGDIAGWVIPVSLIRRQNDNSDIDSFFGESCAPGSDTKSNLCKLCIGDPKNSAANTKCSLSDKEAYYGNQGAFRCLVEKGDVAFVPHTVVFENTDGKNPAVWAKNLKSEDFELLCLDGSRAPVSNYKSCKLSGIPPPAIVTREESISDVVRIVANQQSLYGRKGFEKDMFQLFSSNKGNNLLFNDNTQCLITFDRQPKDIMEDYFGKPYYTTVYGASRSAMSSELISACTIKHCSNSLEVLFQ

Source

organism	Aquarana catesbeiana
common_name	American bullfrog
ncbi_taxonomy_id	8400
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	[(2Z,3aS,4R,6Z,7R,10aS)-10,10-dihydroxy-2,6-diiminooctahydro-1H,8H-pyrrolo[1,2-c]purin-4-yl]methyl benzoate
formula_weight	360.4 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	213

▶

6. Citations (1)

▶

length_a	96.198 Å
length_b	109.335 Å
length_c	254.687 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.450 Å
resolution_low	48.100 Å
r_factor	0.2511
r_work	0.2494
r_free	0.2839

fit	/app/data/saxs_computation/ya/9yas/9yas.fit
pddf	/app/data/pr_computation/ya/9yas/9yas.pr.out
profile	/app/data/saxs_computation/ya/9yas/9yas.dat

Rana catesbeiana saxiphilin mutant - Y558A:STX-C13-OBz (co-crystal)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction