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9vex

Crystal structure of CpaO in complex with beta-CPA

Method: X-RAY DIFFRACTION D_max: 71.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vex
deposition_date	2025-06-10
last_revision	2026-05-27
title	Crystal structure of CpaO in complex with beta-CPA
keywords	FAD-dependent, CPA, CpaO, 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	22.64 Å
rg_electron	21.68 Å
i0	78457200.00
molecular_weight	46731.0 kDa
excluded_volume	45337 Å³
envelope_volume	70967 Å³
shell_volume	26609 Å³
envelope_diameter	71.5 Å
shell_rg	29.16 Å
envelope_rg	21.90 Å
shape_rg	21.63 Å
total_rg	22.39 Å
total_atoms	3548
n_residues	429
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	71.3 Å
rg_real	22.53 Å
rg_real_error	0.38 Å
i0_real	7.8460e+07
i0_real_error	1.0450e+06
rg_reciprocal	22.55 Å
i0_reciprocal	78460000.0000
total_estimate	0.8996
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.2 Å
skewness	0.204
kurtosis	-0.450
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	20200000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Beta-cyclopiazonate dehydrogenase
formula_weight	48511.8 kDa
ec_number	1.21.99.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4027

ARDTISRDVIILGGGSSGTYAAIRLRDQGKTVAVVERNNYLGGHGETYYTEDNTPLNFGVEGFFNTTVTRNYLERLQVPYGRRDPAPAHEDYVNLNTGQRTEYTPGQLQDREAFAKWVDAISQFGFLDDGVYRIPEPVPEDLISPFADFVKKYHLEDAVYALFSHTSGDVLEMITLYVIQYIGVPHAAALNEGYVRPIEGIAALYKSAGKELGSDVLLETTPEAVQRFEDGVEVIVRSADGTKTLLKGKQLLVTIPPLLENLHGFPLSDQESRLFSKWQYHQYWAALVNDTGLPDDVNIVNVDTERLYGVPEEPFIWRLDNHWAPGYHNIKLVGGSEFGEDEAKAYMYERLDLLHAEGTYATHKPEIVKFASHTPVTMFVSAEEIRGGFYRQLYELQGLNSTFWTGATWASDYSTLLWGYTDEVLDQMASS

Source

organism	Aspergillus oryzae
ncbi_taxonomy_id	5062
host_organism	Komagataella phaffii GS115

Entity 2 non-polymer

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

Entity 3 non-polymer

description	2-acetamido-2-deoxy-alpha-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	(3~{Z},5~{S})-5-[[4-(3-methylbut-2-enyl)-1~{H}-indol-3-yl]methyl]-3-(1-oxidanylethylidene)pyrrolidine-2,4-dione
formula_weight	338.4 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	479

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6. Citations (1)

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length_a	118.740 Å
length_b	118.740 Å
length_c	69.204 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 65
int_tables_number	170
crystal_system	—

resolution	1.660 Å
resolution_low	29.900 Å
r_factor	0.1785
r_work	0.1774
r_free	0.1984

fit	/app/data/saxs_computation/ve/9vex/9vex.fit
pddf	/app/data/pr_computation/ve/9vex/9vex.pr.out
profile	/app/data/saxs_computation/ve/9vex/9vex.dat