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9vjx

Structure of the plant diacylglycerol O-acyltransferase 1 H447A mutant

Method: ELECTRON MICROSCOPY D_max: 129.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vjx
deposition_date	2025-06-21
title	Structure of the plant diacylglycerol O-acyltransferase 1 H447A 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	37.10 Å
rg_electron	36.99 Å
i0	287369000.00
molecular_weight	98884.0 kDa
excluded_volume	99678 Å³
envelope_volume	180120 Å³
shell_volume	42250 Å³
envelope_diameter	140.5 Å
shell_rg	40.99 Å
envelope_rg	37.18 Å
shape_rg	36.97 Å
total_rg	37.24 Å
total_atoms	7530
n_residues	841
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	129.8 Å
rg_real	37.46 Å
rg_real_error	1.42 Å
i0_real	2.8740e+08
i0_real_error	5.9580e+06
rg_reciprocal	37.24 Å
i0_reciprocal	287300000.0000
total_estimate	0.5862
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	33.2 Å
skewness	0.539
kurtosis	-0.332
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	29360000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.664; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.675; Smooth: 0.806

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Diacylglycerol O-acyltransferase 1
formula_weight	59962.6 kDa
ec_number	2.3.1.20
mutation	H447A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	7556

MAILDSAGVTTVTENGGGEFVDLDRLRRRKSRSDSSNGLLLSGSDNNSPSDDVGAPADVRDRIDSVVNDDAQGTANLAGDNNGGGDNNGGGRGGGEGRGNADATFTYRPSVPAHRRARESPLSSDAIFKQSHAGLFNLCVVVLIAVNSRLIIENLMKYGWLIRTDFWFSSRSLRDWPLFMCCISLSIFPLAAFTVEKLVLQKYISEPVVIFLHIIITMTEVLYPVYVTLRCDSAFLSGVTLMLLTCIVWLKLVSYAHTSYDIRSLANAADKANPEVSYYVSLKSLAYFMVAPTLCYQPSYPRSACIRKGWVARQFAKLVIFTGFMGFIIEQYINPIVRNSKHPLKGDLLYAIERVLKLSVPNLYVWLCMFYCFFHLWLNILAELLCFGDREFYKDWWNAKSVGDYWRMWNMPVHKWMVRHIYFPCLRSKIPKTLAIIIAFLVSAVFAELCIAVPCRLFKLWAFLGIMFQVPLVFITNYLQERFGSTVGNMIFWFIFCIFGQPMCVLLYYHDLMNRKGSMSGPHHHHHH

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
ec_number	2.3.1.20
src_method	man
entity_count	9

Entity 3 non-polymer

description	COENZYME A
formula_weight	767.5 kDa
src_method	syn
entity_count	1

Entity 4 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	1

Entity 5 non-polymer

description	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
formula_weight	648.9 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	[(2~{S})-2-[(~{Z})-octadec-9-enoyl]oxy-3-oxidanyl-propyl] (~{Z})-octadec-9-enoate
formula_weight	621.0 kDa
src_method	syn
entity_count	4

Entity 7 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	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	6

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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	2.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.60 Å
resolution_method	—
num_particles	67838

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