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9qso

Tetrapodal ancestor of L-amino acid oxidases co-crystallised with indole-3-pyruvate

Method: X-RAY DIFFRACTION D_max: 77.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qso
deposition_date	2025-04-06
last_revision	2026-04-15
title	Tetrapodal ancestor of L-amino acid oxidases co-crystallised with indole-3-pyruvate
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	24.30 Å
rg_electron	23.24 Å
i0	51208800.00
molecular_weight	55896.0 kDa
excluded_volume	70093 Å³
envelope_volume	80297 Å³
shell_volume	28466 Å³
envelope_diameter	80.2 Å
shell_rg	30.86 Å
envelope_rg	23.44 Å
shape_rg	23.21 Å
total_rg	24.21 Å
total_atoms	3950
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	77.4 Å
rg_real	24.22 Å
rg_real_error	0.38 Å
i0_real	5.1210e+07
i0_real_error	6.7100e+05
rg_reciprocal	24.24 Å
i0_reciprocal	51210000.0000
total_estimate	0.8995
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.2 Å
skewness	0.265
kurtosis	-0.405
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	12050000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.984

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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 acid oxidases co-crystallised
formula_weight	55440.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3991

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	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	32

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6. Citations (1)

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length_a	95.532 Å
length_b	95.532 Å
length_c	187.607 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	2.980 Å
resolution_low	47.810 Å
r_factor	0.2236
r_work	0.2202
r_free	0.2891

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