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9vk0

Structure of the plant diacylglycerol O-acyltransferase 1 in complex with triacylglycerol and free fatty acid

Method: ELECTRON MICROSCOPY D_max: 107.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vk0
deposition_date	2025-06-22
title	Structure of the plant diacylglycerol O-acyltransferase 1 in complex with triacylglycerol and free fatty acid
keywords	TAG synthysis, activity regulation, FFA, intramembrane enzyme, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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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	31.21 Å
rg_electron	30.88 Å
i0	190036000.00
molecular_weight	79755.0 kDa
excluded_volume	80630 Å³
envelope_volume	141810 Å³
shell_volume	38407 Å³
envelope_diameter	121.4 Å
shell_rg	37.60 Å
envelope_rg	31.45 Å
shape_rg	30.89 Å
total_rg	31.34 Å
total_atoms	6076
n_residues	710
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	107.0 Å
rg_real	31.32 Å
rg_real_error	0.81 Å
i0_real	1.9000e+08
i0_real_error	2.9810e+06
rg_reciprocal	31.27 Å
i0_reciprocal	190000000.0000
total_estimate	0.8608
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.6 Å
skewness	0.475
kurtosis	-0.224
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	21250000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.919; Smooth: 0.954

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Diacylglycerol O-acyltransferase 1
formula_weight	60029.7 kDa
ec_number	2.3.1.20
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6076

MAILDSAGVTTVTENGGGEFVDLDRLRRRKSRSDSSNGLLLSGSDNNSPSDDVGAPADVRDRIDSVVNDDAQGTANLAGDNNGGGDNNGGGRGGGEGRGNADATFTYRPSVPAHRRARESPLSSDAIFKQSHAGLFNLCVVVLIAVNSRLIIENLMKYGWLIRTDFWFSSRSLRDWPLFMCCISLSIFPLAAFTVEKLVLQKYISEPVVIFLHIIITMTEVLYPVYVTLRCDSAFLSGVTLMLLTCIVWLKLVSYAHTSYDIRSLANAADKANPEVSYYVSLKSLAYFMVAPTLCYQPSYPRSACIRKGWVARQFAKLVIFTGFMGFIIEQYINPIVRNSKHPLKGDLLYAIERVLKLSVPNLYVWLCMFYCFFHLWLNILAELLCFGDREFYKDWWNAKSVGDYWRMWNMPVHKWMVRHIYFPCLRSKIPKTLAIIIAFLVSAVFHELCIAVPCRLFKLWAFLGIMFQVPLVFITNYLQERFGSTVGNMIFWFIFCIFGQPMCVLLYYHDLMNRKGSMSGPHHHHHH

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Komagataella pastoris

Entity 2 non-polymer

description	OLEIC ACID
formula_weight	282.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	2,3-bis[[(Z)-octadec-9-enoyl]oxy]propyl (Z)-octadec-9-enoate
formula_weight	885.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.010 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.01 Å
resolution_method	—
num_particles	171030

fit	/app/data/saxs_computation/vk/9vk0/9vk0.fit
pddf	/app/data/pr_computation/vk/9vk0/9vk0.pr.out
profile	/app/data/saxs_computation/vk/9vk0/9vk0.dat

Structure of the plant diacylglycerol O-acyltransferase 1 in complex with triacylglycerol and free fatty acid

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

EM 3D