SAXSdb — 9w1b

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1. Structure Basics

entry_id	9w1b
deposition_date	2025-07-25
title	Cryo-EM structure of a Fungal XPR1 with InsP6
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	36.95 Å
rg_electron	36.31 Å
i0	279708000.00
molecular_weight	144520.0 kDa
excluded_volume	184510 Å³
envelope_volume	248160 Å³
shell_volume	55440 Å³
envelope_diameter	113.2 Å
shell_rg	44.03 Å
envelope_rg	35.46 Å
shape_rg	36.30 Å
total_rg	36.88 Å
total_atoms	10194
n_residues	1144
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	110.8 Å
rg_real	36.71 Å
rg_real_error	0.71 Å
i0_real	2.7970e+08
i0_real_error	4.8020e+06
rg_reciprocal	36.86 Å
i0_reciprocal	279700000.0000
total_estimate	0.9115
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	46.4 Å
skewness	0.017
kurtosis	-0.728
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	27200000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.948

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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,E
atom_count	10194

MDYKDDDDKGGSGSGGSGSGSSGSTGKFGKVIEGQSVAEWASAYFDYKKGKKIIAGIAKNPSEGLYGTSGILGETPEEAIVKRGQIHRFHPLFQEFLDQQANKVEEFFENLVSDARERMDLISDQVDIYEKLRAFKKGTLESGSVVLIQKQHSKLRQRLDSILNFSRLQPAYHIPARKSVPTDAYTPMVSYRKLKSKLKTTLLDFYDYLKLVSQYQHLNQQAFRKIVKKYDKTLHTDLQGFWVDYMSRYTFTDFSITTNWQLHVEDIYARLFTNHNKKLALEHLKSFRQKEHFSANSMRFGLLFGAGLPLAIEAACYYNATEQSSYLLQIWGGFFLVIFAFVLFDLDCYVWEKTRVNYMLIFEFNQRKSLNWRQHLEIVGAVFFIFSLFFFLCMRNFFPGFTIYFPALFLGVVGTFLIAPVIVPYWRMRRYLIIQLIRVFLSGLSTVHFQDFFFADQMVSLTYACGNISLFFCLYKRLWRQPQLCNSSHSPLLGFFTTLPGILRVFQCFRRYSDSLKSFPHLVNALKYIFNILAQMFLSLWRIHPGLKYRVLYTIFAGVNSLFSYTWDILMDWNLLVRKDGRWQFREHRILKQLWPYIIAMILNFIVRSSFIFYCIFPNHIQHSSGISFFVTLAEIMRRCMWNILRVEHEEIYNRENLRAARELKPLDFVKPHSDVFVSHQISSDKNYTDDEDSMDDQTDVDEAQFS

Source

organism	Schizosaccharomyces pombe 972h-
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	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	4

Entity 5 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	2.87 Å
resolution_method	—
num_particles	226844

fit	/app/data/saxs_computation/w1/9w1b/9w1b.fit
pddf	/app/data/pr_computation/w1/9w1b/9w1b.pr.out
profile	/app/data/saxs_computation/w1/9w1b/9w1b.dat

Cryo-EM structure of a Fungal XPR1 with InsP6

SAXS Profile

P(r) Distribution