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9vl3

Cryo-EM structure of human lipid phosphate phosphatase 1 complexed with PO4 in nanodiscs

Method: ELECTRON MICROSCOPY D_max: 93.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vl3
deposition_date	2025-06-24
title	Cryo-EM structure of human lipid phosphate phosphatase 1 complexed with PO4 in nanodiscs
keywords	phosphatase, 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	31.15 Å
rg_electron	29.63 Å
i0	201202000.00
molecular_weight	123650.0 kDa
excluded_volume	159080 Å³
envelope_volume	181540 Å³
shell_volume	48323 Å³
envelope_diameter	99.2 Å
shell_rg	38.84 Å
envelope_rg	29.83 Å
shape_rg	29.62 Å
total_rg	30.48 Å
total_atoms	8692
n_residues	1008
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	93.5 Å
rg_real	30.90 Å
rg_real_error	0.50 Å
i0_real	2.0120e+08
i0_real_error	2.9070e+06
rg_reciprocal	31.01 Å
i0_reciprocal	201200000.0000
total_estimate	0.8969
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	42.1 Å
skewness	0.057
kurtosis	-0.427
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	21030000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.946

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Phospholipid phosphatase 1
formula_weight	32126.0 kDa
ec_number	3.1.3.-,3.1.3.106,3.1.3.4,3.6.1.75
mutation	H223A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	8692

MFDKTRLPYVALDVLCVLLAGLPFAILTSRHTPFQRGVFCNDESIKYPYKEDTIPYALLGGIIIPFSIIVIILGETLSVYCNLLHSNSFIRNNYIATIYKAIGTFLFGAAASQSLTDIAKYSIGRLRPHFLDVCDPDWSKINCSDGYIEYYICRGNAERVKEGRLSFYSGHSSFSMYCMLFVALYLQARMKGDWARLLRPTLQFGLVAVSIYVGLSRVSDYKAHWSDVLTGLIQGALVAILVAVYVSDFFKERTSFKERKEEDSHTTLHETPTTGNHYPSNHQP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
formula_weight	648.9 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
formula_weight	760.1 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	;[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate ;
formula_weight	1047.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	4

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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	2.820 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.82 Å
resolution_method	—
num_particles	189213

fit	/app/data/saxs_computation/vl/9vl3/9vl3.fit
pddf	/app/data/pr_computation/vl/9vl3/9vl3.pr.out
profile	/app/data/saxs_computation/vl/9vl3/9vl3.dat