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9y6k

Avermitilol synthase T215V: Complex with Mg, inorganic pyrophosphate, and benzyltriethyl ammonium cation

Method: X-RAY DIFFRACTION D_max: 62.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y6k
deposition_date	2025-09-08
title	Avermitilol synthase T215V: Complex with Mg, inorganic pyrophosphate, and benzyltriethyl ammonium cation
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	20.03 Å
rg_electron	18.94 Å
i0	24205400.00
molecular_weight	36241.0 kDa
excluded_volume	44750 Å³
envelope_volume	50455 Å³
shell_volume	21777 Å³
envelope_diameter	62.7 Å
shell_rg	25.90 Å
envelope_rg	19.20 Å
shape_rg	18.92 Å
total_rg	19.88 Å
total_atoms	2548
n_residues	331
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	62.1 Å
rg_real	19.92 Å
rg_real_error	0.32 Å
i0_real	2.4210e+07
i0_real_error	3.2190e+05
rg_reciprocal	19.94 Å
i0_reciprocal	24210000.0000
total_estimate	0.8986
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.6 Å
skewness	0.162
kurtosis	-0.404
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	7961000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Avermitilol synthase
formula_weight	36836.6 kDa
ec_number	4.2.3.96
mutation	T215V
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2766

SNIMPQDIDFGLPAPAGISPGLEATRRHNLGWVRRLGLVGDGPSLAWYTSWDMPRLAACGFPHARGAALDLCADAMAFFFVFDDQFDGPLGRDPARAARVCRRLTGIVHGAGPGPGADACSAAFADVWARSTDGAHPGWVARTAHEWEYYFAAQAHEAINRLRGTPGDMESYLQVRRGIAGTDLPLSLGERAAGITVPAAAFHSPQLRIMREAAIDVVLMCNDVYSLEKEEARGDMDNLVLVIEHARRCTRDEAVTAARGEVARRVIRFEQLAREVPALCAQLGLSAVERAHVDTYLGVMEAWMSGYHAWQTQTRRYTGAPHVLPSTGPGYFDEVLPT

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	N-benzyl-N,N-diethylethanaminium
formula_weight	192.3 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	207

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6. Citations (1)

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length_a	95.373 Å
length_b	56.503 Å
length_c	72.557 Å
angle_alpha	90.00 °
angle_beta	125.15 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.420 Å
resolution_low	31.460 Å
r_factor	0.1853
r_work	0.1844
r_free	0.2015

fit	/app/data/saxs_computation/y6/9y6k/9y6k.fit
pddf	/app/data/pr_computation/y6/9y6k/9y6k.pr.out
profile	/app/data/saxs_computation/y6/9y6k/9y6k.dat