Crystal Structure of avermectin oxidase

Method: X-RAY DIFFRACTION D_max: 100.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v2t
deposition_date	2025-05-20
last_revision	2026-05-27
title	Crystal Structure of avermectin oxidase
keywords	oxidase, P450, avermectin, 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	31.41 Å
rg_electron	30.48 Å
i0	141583000.00
molecular_weight	93508.0 kDa
excluded_volume	116640 Å³
envelope_volume	146310 Å³
shell_volume	39494 Å³
envelope_diameter	102.6 Å
shell_rg	38.11 Å
envelope_rg	30.23 Å
shape_rg	30.49 Å
total_rg	31.09 Å
total_atoms	6588
n_residues	824
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	100.4 Å
rg_real	31.34 Å
rg_real_error	0.84 Å
i0_real	1.4160e+08
i0_real_error	2.4450e+06
rg_reciprocal	31.37 Å
i0_reciprocal	141600000.0000
total_estimate	0.9009
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	38.2 Å
skewness	0.258
kurtosis	-0.469
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	38090000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.958

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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6. Citations (1)

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length_a	176.614 Å
length_b	47.540 Å
length_c	107.834 Å
angle_alpha	90.00 °
angle_beta	99.82 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	3.150 Å
resolution_low	42.250 Å
r_factor	—
r_work	0.2527
r_free	0.3082

description	Cytochrome P450 monooxygenase CYP107Z12
formula_weight	48109.7 kDa
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	6588

Crystal Structure of avermectin oxidase

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Streptomyces tubercidicus
ncbi_taxonomy_id	47759
host_organism	Escherichia coli

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

fit	/app/data/saxs_computation/v2/9v2t/9v2t.fit
pddf	/app/data/pr_computation/v2/9v2t/9v2t.pr.out
profile	/app/data/saxs_computation/v2/9v2t/9v2t.dat