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9ybd

Rana catesbeiana saxiphilin mutant - F561A:STX-C13-OBz (co-crystal)

Method: X-RAY DIFFRACTION D_max: 147.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ybd
deposition_date	2025-09-17
last_revision	2026-05-27
title	Rana catesbeiana saxiphilin mutant - F561A:STX-C13-OBz (co-crystal)
keywords	Saxiphilin, Toxin resistance, Saxitoxin, ANTITOXIN; ANTITOXIN
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	44.76 Å
rg_electron	44.44 Å
i0	1010430000.00
molecular_weight	170400.0 kDa
excluded_volume	162630 Å³
envelope_volume	334690 Å³
shell_volume	62218 Å³
envelope_diameter	150.7 Å
shell_rg	49.91 Å
envelope_rg	43.34 Å
shape_rg	44.43 Å
total_rg	44.62 Å
total_atoms	12800
n_residues	1654
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	147.9 Å
rg_real	44.75 Å
rg_real_error	1.35 Å
i0_real	1.0100e+09
i0_real_error	1.8140e+07
rg_reciprocal	44.76 Å
i0_reciprocal	1010000000.0000
total_estimate	0.8927
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	50.7 Å
skewness	0.264
kurtosis	-0.537
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	28500000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.833

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Saxiphilin
formula_weight	94152.2 kDa
mutation	F561A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	12862

MAPTFQTALFFTIISLSFAAPNAKQVRWCAISDLEQKKCNDLVGSCNVPDITLVCVLRSSTEDCMTAIKDGQADAMFLDSGEVYEASKDPYNLKPIIAEPYSSNRDLQKCLKERQQALAKKMIGHYIPQCDEKGNYQPQQCHGSTGHCWCVNAMGEKISGTNTPPGQTRATCERHELPKCLKERQVALGGDEKVLGRFVPQCDEKGNYEPQQFHGSTGYSWCVNAIGEEIAGTKTPPGKIPATCQKHDLVTTCHYAVAMVKKSSAFQFNQLKGKRSCHSGVSKTDGWKALVTVLVEKKLLSWDGPAKESIQRAMSKFFSVSCIPGATQTNLCKQCKGEEGKNCKNSHDEPYYGNYGAFRCLKEDMGDVAFLRSTALSDEHSEVYELLCPDNTRKPLNKYKECNLGTVPAGTVVTRKISDKTEDINNFLMEAQKRQCKLFSSAHGKDLMFDDSTLQLALLSSEVDAFLYLGVKLFHAMKALTGDAHLPSKNKVRWCTINKLEKMKCDDWSAVSGGAIACTEASCPKGCVKQILKGEADAVKLEVQYMYEALMCGLLPAVEEYHNKDDFGPCKTPGSPYTDAGTLRAVALVKKSNKDINWNNIKGKKSCHTGVGDIAGWVIPVSLIRRQNDNSDIDSFFGESCAPGSDTKSNLCKLCIGDPKNSAANTKCSLSDKEAYYGNQGAFRCLVEKGDVAFVPHTVVFENTDGKNPAVWAKNLKSEDFELLCLDGSRAPVSNYKSCKLSGIPPPAIVTREESISDVVRIVANQQSLYGRKGFEKDMFQLFSSNKGNNLLFNDNTQCLITFDRQPKDIMEDYFGKPYYTTVYGASRSAMSSELISACTIKHCSNSLEVLFQ

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	62

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6. Citations (1)

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length_a	96.424 Å
length_b	110.042 Å
length_c	256.010 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	2.400 Å
resolution_low	48.210 Å
r_factor	0.2305
r_work	0.2290
r_free	0.2582

fit	/app/data/saxs_computation/yb/9ybd/9ybd.fit
pddf	/app/data/pr_computation/yb/9ybd/9ybd.pr.out
profile	/app/data/saxs_computation/yb/9ybd/9ybd.dat

Rana catesbeiana saxiphilin mutant - F561A: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