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9qs1

Tetrapodal ancestor of L-amino acid oxidases

Method: X-RAY DIFFRACTION D_max: 78.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qs1
deposition_date	2025-04-04
last_revision	2026-04-15
title	Tetrapodal ancestor of L-amino acid oxidases
keywords	tryptophan, metabolic signaling, oxidation, FAD, snake venom, immunometabolism, OXIDOREDUCTASE; OXIDOREDUCTASE
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	24.28 Å
rg_electron	23.23 Å
i0	50952500.00
molecular_weight	55691.0 kDa
excluded_volume	69794 Å³
envelope_volume	81111 Å³
shell_volume	28677 Å³
envelope_diameter	80.4 Å
shell_rg	30.90 Å
envelope_rg	23.46 Å
shape_rg	23.19 Å
total_rg	24.21 Å
total_atoms	3936
n_residues	483
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	78.3 Å
rg_real	24.19 Å
rg_real_error	0.43 Å
i0_real	5.0950e+07
i0_real_error	6.8410e+05
rg_reciprocal	24.21 Å
i0_reciprocal	50950000.0000
total_estimate	0.8964
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.260
kurtosis	-0.412
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	13380000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Tetrapodal ancestor of L-amino acis oxidases
formula_weight	55440.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3997

MESSDDPLDKCFQDPDYEELLEIAKHGLRKTTKPKRVVIVGAGIAGLTAAKVLEDAGHKVTILEASDRVGGRVLTYRNESEGWYAELGAMRIPSFHRIVHTFIKKLGLKLNEFIQYDINTWYFVNGVRKRTYAVKDNPDVLNYPVRPSEKGKSADQLYQEALQKVLEDLKRSGCKKVLKKYDSYSVKEYLIKEGNLSRGAVRMIGDLLNEDSFFYISFTESLRIQSDINDNVRYYEITGGFDNLPRAFYQSLSGPVHLNSRVVRINQNKRGVTVFYRDQQESSLSNITADYVLLTTTAKATRLIDFQPPLSPKKTHALRSVHYSSSTKIFLSFRQRFWEKEGIHGGKSITDRPSRFIYYPSHSFPSSGGVLLASYTWSDDSDFFLGLSDEECMQVALDDLAKIHGLPKEQIRSLWDGTGVVKKWSLDPYSLGAFAAFTPYQLTDYAKELFQSEGRVHFAGEHTALPHGWIETSMKSALRAARNIHNAA

Source

organism	Tetrapoda
ncbi_taxonomy_id	32523
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	NITRATE ION
formula_weight	62.0 kDa
src_method	nat
entity_count	1

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	61

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6. Citations (1)

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length_a	94.515 Å
length_b	94.515 Å
length_c	190.062 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.500 Å
resolution_low	84.630 Å
r_factor	0.2070
r_work	0.2049
r_free	0.2458

fit	/app/data/saxs_computation/qs/9qs1/9qs1.fit
pddf	/app/data/pr_computation/qs/9qs1/9qs1.pr.out
profile	/app/data/saxs_computation/qs/9qs1/9qs1.dat