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9vjm

Structure of the plant diacylglycerol O-acyltransferase 1 C246A mutant

Method: ELECTRON MICROSCOPY D_max: 111.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vjm
deposition_date	2025-06-21
title	Structure of the plant diacylglycerol O-acyltransferase 1 C246A mutant
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	31.86 Å
rg_electron	31.51 Å
i0	191979000.00
molecular_weight	80207.0 kDa
excluded_volume	81120 Å³
envelope_volume	147400 Å³
shell_volume	39398 Å³
envelope_diameter	121.9 Å
shell_rg	37.85 Å
envelope_rg	31.77 Å
shape_rg	31.51 Å
total_rg	31.94 Å
total_atoms	6116
n_residues	718
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	111.0 Å
rg_real	31.97 Å
rg_real_error	0.99 Å
i0_real	1.9200e+08
i0_real_error	3.1430e+06
rg_reciprocal	31.93 Å
i0_reciprocal	192000000.0000
total_estimate	0.8605
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.3 Å
skewness	0.461
kurtosis	-0.240
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	24240000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.751; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.960

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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	59997.6 kDa
ec_number	2.3.1.20
mutation	C246A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6116

MAILDSAGVTTVTENGGGEFVDLDRLRRRKSRSDSSNGLLLSGSDNNSPSDDVGAPADVRDRIDSVVNDDAQGTANLAGDNNGGGDNNGGGRGGGEGRGNADATFTYRPSVPAHRRARESPLSSDAIFKQSHAGLFNLCVVVLIAVNSRLIIENLMKYGWLIRTDFWFSSRSLRDWPLFMCCISLSIFPLAAFTVEKLVLQKYISEPVVIFLHIIITMTEVLYPVYVTLRCDSAFLSGVTLMLLTAIVWLKLVSYAHTSYDIRSLANAADKANPEVSYYVSLKSLAYFMVAPTLCYQPSYPRSACIRKGWVARQFAKLVIFTGFMGFIIEQYINPIVRNSKHPLKGDLLYAIERVLKLSVPNLYVWLCMFYCFFHLWLNILAELLCFGDREFYKDWWNAKSVGDYWRMWNMPVHKWMVRHIYFPCLRSKIPKTLAIIIAFLVSAVFHELCIAVPCRLFKLWAFLGIMFQVPLVFITNYLQERFGSTVGNMIFWFIFCIFGQPMCVLLYYHDLMNRKGSMSGPHHHHHH

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	3.28 Å
resolution_method	—
num_particles	224579

fit	/app/data/saxs_computation/vj/9vjm/9vjm.fit
pddf	/app/data/pr_computation/vj/9vjm/9vjm.pr.out
profile	/app/data/saxs_computation/vj/9vjm/9vjm.dat