SAXSdb — 9w0x

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1. Structure Basics

entry_id	9w0x
deposition_date	2025-07-24
title	Cryo-EM structure of a Fungal XPR1
keywords	phosphate exporter, dimer, membrane protein, TRANSPORT PROTEIN; TRANSPORT 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	37.43 Å
rg_electron	36.74 Å
i0	273891000.00
molecular_weight	147360.0 kDa
excluded_volume	189880 Å³
envelope_volume	255420 Å³
shell_volume	56250 Å³
envelope_diameter	116.1 Å
shell_rg	44.39 Å
envelope_rg	36.01 Å
shape_rg	36.72 Å
total_rg	37.37 Å
total_atoms	10436
n_residues	1190
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	111.4 Å
rg_real	37.20 Å
rg_real_error	0.72 Å
i0_real	2.7390e+08
i0_real_error	4.3980e+06
rg_reciprocal	37.35 Å
i0_reciprocal	273900000.0000
total_estimate	0.9095
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	42.4 Å
skewness	0.025
kurtosis	-0.723
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	20650000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.907

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Protein SYG1 homolog
formula_weight	82913.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	10436

MDYKDDDDKGGSGSGGSGSGSSGSTGKFGKVIEGQSVAEWASAYFDYKKGKKIIAGIAKNPSEGLYGTSGILGETPEEAIVKRGQIHRFHPLFQEFLDQQANKVEEFFENLVSDARERMDLISDQVDIYEKLRAFKKGTLESGSVVLIQKQHSKLRQRLDSILNFSRLQPAYHIPARKSVPTDAYTPMVSYRKLKSKLKTTLLDFYDYLKLVSQYQHLNQQAFRKIVKKYDKTLHTDLQGFWVDYMSRYTFTDFSITTNWQLHVEDIYARLFTNHNKKLALEHLKSFRQKEHFSANSMRFGLLFGAGLPLAIEAACYYNATEQSSYLLQIWGGFFLVIFAFVLFDLDCYVWEKTRVNYMLIFEFNQRKSLNWRQHLEIVGAVFFIFSLFFFLCMRNFFPGFTIYFPALFLGVVGTFLIAPVIVPYWRMRRYLIIQLIRVFLSGLSTVHFQDFFFADQMVSLTYACGNISLFFCLYKRLWRQPQLCNSSHSPLLGFFTTLPGILRVFQCFRRYSDSLKSFPHLVNALKYIFNILAQMFLSLWRIHPGLKYRVLYTIFAGVNSLFSYTWDILMDWNLLVRKDGRWQFREHRILKQLWPYIIAMILNFIVRSSFIFYCIFPNHIQHSSGISFFVTLAEIMRRCMWNILRVEHEEIYNRENLRAARELKPLDFVKPHSDVFVSHQISSDKNYTDDEDSMDDQTDVDEAQFS

Source

organism	Schizosaccharomyces pombe (strain 972 / ATCC 24843)
common_name	fission yeast
ncbi_taxonomy_id	284812
host_organism	Homo sapiens

Entity 2 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	18

Entity 3 non-polymer

description	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
formula_weight	692.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
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	2.90 Å
resolution_method	—
num_particles	210108

fit	/app/data/saxs_computation/w0/9w0x/9w0x.fit
pddf	/app/data/pr_computation/w0/9w0x/9w0x.pr.out
profile	/app/data/saxs_computation/w0/9w0x/9w0x.dat

Cryo-EM structure of a Fungal XPR1

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

EM 3D