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9rfz

Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with tetradecane

Method: X-RAY DIFFRACTION D_max: 84.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rfz
deposition_date	2025-06-05
last_revision	2026-04-01
title	Unspecific peroxygenase from Psathyrella aberdarensis, Grogu variant, in complex with tetradecane
keywords	Peroxygenase, peroxidase, OXIDOREDUCTASE, complex, tetradecane; 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	27.33 Å
rg_electron	26.46 Å
i0	101522000.00
molecular_weight	78127.0 kDa
excluded_volume	96879 Å³
envelope_volume	113720 Å³
shell_volume	34902 Å³
envelope_diameter	88.8 Å
shell_rg	34.52 Å
envelope_rg	26.53 Å
shape_rg	26.45 Å
total_rg	27.30 Å
total_atoms	5474
n_residues	668
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	84.6 Å
rg_real	27.23 Å
rg_real_error	0.49 Å
i0_real	1.0150e+08
i0_real_error	1.2990e+06
rg_reciprocal	27.26 Å
i0_reciprocal	101500000.0000
total_estimate	0.9053
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.1 Å
skewness	0.249
kurtosis	-0.472
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	19500000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.964

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Heme-thiolate peroxidase
formula_weight	36575.5 kDa
ec_number	1.11.2.1
mutation	S61A, L79I, A252L
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5736

LNEVDPPTPPGPLAYNGTKLVHDDAHPFKAPEQGDIRGPCPGLNTLANHGYLPHNGVATPAQIIEAVQEGFNMEHATAIFVTYAAHLVDGNLVTDLLSIGEKTGLTGLDPPAPAIVGGLNTHAVFEGDASMTRADFFFGDNHNFNQTLFDQFVDFSNRFGGGFYNYTVAAELRFQRIQESIATNPQFSFISPRFFTAYAESTFPVNFFVDGRSTEKKLDMEAATSFIRDGKYPQDFHRAAQPSSTEGIDIVLSAHPVAPGENRDGKINNYVPDPTSADFSTFCLLYTNFVNQTIGGLYPNPTGVLRRNLIKNLRFFYSGIADAGCEELFPYGQL

Source

organism	Candolleomyces aberdarensis
ncbi_taxonomy_id	2316362
host_organism	Komagataella phaffii CBS 7435

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	3

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	4

Entity 4 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	14

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	TETRADECANE
formula_weight	198.4 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	248

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6. Citations (1)

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length_a	76.753 Å
length_b	76.753 Å
length_c	266.286 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65
int_tables_number	170
crystal_system	—

resolution	2.120 Å
resolution_low	47.040 Å
r_factor	0.2203
r_work	0.2185
r_free	0.2534

fit	/app/data/saxs_computation/rf/9rfz/9rfz.fit
pddf	/app/data/pr_computation/rf/9rfz/9rfz.pr.out
profile	/app/data/saxs_computation/rf/9rfz/9rfz.dat