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9vk1

Structure of the plant diacylglycerol O-acyltransferase 1 in complex with oleoyl-CoA

Method: ELECTRON MICROSCOPY D_max: 109.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vk1
deposition_date	2025-06-22
title	Structure of the plant diacylglycerol O-acyltransferase 1 in complex with oleoyl-CoA
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	32.90 Å
rg_electron	32.60 Å
i0	106212000.00
molecular_weight	91099.0 kDa
excluded_volume	117790 Å³
envelope_volume	154060 Å³
shell_volume	39831 Å³
envelope_diameter	115.4 Å
shell_rg	38.65 Å
envelope_rg	32.79 Å
shape_rg	32.57 Å
total_rg	33.27 Å
total_atoms	6418
n_residues	760
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	109.3 Å
rg_real	33.01 Å
rg_real_error	0.85 Å
i0_real	1.0620e+08
i0_real_error	1.5520e+06
rg_reciprocal	32.97 Å
i0_reciprocal	106200000.0000
total_estimate	0.8717
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	34.1 Å
skewness	0.431
kurtosis	-0.332
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	18540000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.850

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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	6418

MAILDSAGVTTVTENGGGEFVDLDRLRRRKSRSDSSNGLLLSGSDNNSPSDDVGAPADVRDRIDSVVNDDAQGTANLAGDNNGGGDNNGGGRGGGEGRGNADATFTYRPSVPAHRRARESPLSSDAIFKQSHAGLFNLCVVVLIAVNSRLIIENLMKYGWLIRTDFWFSSRSLRDWPLFMCCISLSIFPLAAFTVEKLVLQKYISEPVVIFLHIIITMTEVLYPVYVTLRCDSAFLSGVTLMLLTCIVWLKLVSYAHTSYDIRSLANAADKANPEVSYYVSLKSLAYFMVAPTLCYQPSYPRSACIRKGWVARQFAKLVIFTGFMGFIIEQYINPIVRNSKHPLKGDLLYAIERVLKLSVPNLYVWLCMFYCFFHLWLNILAELLCFGDREFYKDWWNAKSVGDYWRMWNMPVHKWMVRHIYFPCLRSKIPKTLAIIIAFLVSAVFHELCIAVPCRLFKLWAFLGIMFQVPLVFITNYLQERFGSTVGNMIFWFIFCIFGQPMCVLLYYHDLMNRKGSMSGPHHHHHH

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Komagataella pastoris

Entity 2 non-polymer

description	;S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name) ;
formula_weight	1032.0 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	3.540 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.54 Å
resolution_method	—
num_particles	462401

fit	/app/data/saxs_computation/vk/9vk1/9vk1.fit
pddf	/app/data/pr_computation/vk/9vk1/9vk1.pr.out
profile	/app/data/saxs_computation/vk/9vk1/9vk1.dat

Structure of the plant diacylglycerol O-acyltransferase 1 in complex with oleoyl-CoA

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

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)