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9y6j

Avermitilol synthase: Complex with Mg, inorganic pyrophosphate, and bicyclic tetralin-based tertiary amine

Method: X-RAY DIFFRACTION D_max: 61.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y6j
deposition_date	2025-09-08
title	Avermitilol synthase: Complex with Mg, inorganic pyrophosphate, and bicyclic tetralin-based tertiary amine
keywords	Biosynthesis, Terpene, Cyclization, LYASE; LYASE
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	19.87 Å
rg_electron	18.90 Å
i0	44483400.00
molecular_weight	33882.0 kDa
excluded_volume	32319 Å³
envelope_volume	50536 Å³
shell_volume	21817 Å³
envelope_diameter	62.9 Å
shell_rg	25.91 Å
envelope_rg	19.18 Å
shape_rg	18.90 Å
total_rg	19.56 Å
total_atoms	2556
n_residues	332
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	61.6 Å
rg_real	19.73 Å
rg_real_error	0.29 Å
i0_real	4.4480e+07
i0_real_error	5.0040e+05
rg_reciprocal	19.75 Å
i0_reciprocal	44480000.0000
total_estimate	0.8984
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.0 Å
skewness	0.177
kurtosis	-0.397
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	12790000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Avermitilol synthase
formula_weight	36838.6 kDa
ec_number	4.2.3.96
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2788

SNIMPQDIDFGLPAPAGISPGLEATRRHNLGWVRRLGLVGDGPSLAWYTSWDMPRLAACGFPHARGAALDLCADAMAFFFVFDDQFDGPLGRDPARAARVCRRLTGIVHGAGPGPGADACSAAFADVWARSTDGAHPGWVARTAHEWEYYFAAQAHEAINRLRGTPGDMESYLQVRRGIAGTDLPLSLGERAAGITVPAAAFHSPQLRIMREAAIDVTLMCNDVYSLEKEEARGDMDNLVLVIEHARRCTRDEAVTAARGEVARRVIRFEQLAREVPALCAQLGLSAVERAHVDTYLGVMEAWMSGYHAWQTQTRRYTGAPHVLPSTGPGYFDEVLPT

Source

organism	Streptomyces avermitilis
ncbi_taxonomy_id	33903
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	(2S)-N,N-dimethyl-1,2,3,4-tetrahydronaphthalen-2-amine
formula_weight	175.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIPHOSPHATE
formula_weight	173.9 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	232

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6. Citations (1)

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length_a	95.552 Å
length_b	56.374 Å
length_c	72.612 Å
angle_alpha	90.00 °
angle_beta	125.31 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.440 Å
resolution_low	31.400 Å
r_factor	0.1758
r_work	0.1747
r_free	0.1971

fit	/app/data/saxs_computation/y6/9y6j/9y6j.fit
pddf	/app/data/pr_computation/y6/9y6j/9y6j.pr.out
profile	/app/data/saxs_computation/y6/9y6j/9y6j.dat