Cryo-EM structure of Oryza sativa phosphate transporter SPDT

Method: ELECTRON MICROSCOPY D_max: 114.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u9f
deposition_date	2025-03-27
title	Cryo-EM structure of Oryza sativa phosphate transporter SPDT
keywords	phosphate transport, SPDT, SLC26, SULTR, cryo-EM, 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	35.10 Å
rg_electron	35.03 Å
i0	191823000.00
molecular_weight	119610.0 kDa
excluded_volume	153330 Å³
envelope_volume	194840 Å³
shell_volume	46082 Å³
envelope_diameter	122.8 Å
shell_rg	41.75 Å
envelope_rg	34.88 Å
shape_rg	35.05 Å
total_rg	35.45 Å
total_atoms	8400
n_residues	1118
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	114.9 Å
rg_real	35.10 Å
rg_real_error	0.78 Å
i0_real	1.9180e+08
i0_real_error	3.0770e+06
rg_reciprocal	35.10 Å
i0_reciprocal	191800000.0000
total_estimate	0.8907
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.8 Å
skewness	0.291
kurtosis	-0.562
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	43640000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	SULTR-like phosphorus distribution transporter
formula_weight	72054.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8400

MVVNNKVDSLSYDVEAPPAQAPTTPAVVSAPPTPRGEAPAMTTTAAAELHKVSVPERRSTAKALRQRLAEVFFPDDPLHQFKNQSSARRLVLALQYFFPIFHWGSDYSLRLLRSDVVSGLTIASLAIPQGISYAKLANLPPIIGLYSSFVPPLIYSLLGSSRDLAVGPVSIASLVMGSMLRQAVSPDQEPILYLQLAFTSTFFAGVFQASLGFLRLGFIVDFLSKATLTGFMGGAAIIVSLQQLKGLLGIIHFTSQMGFVQVMHSVFKHHDEWAWQTILMGVAFLAVLLTTRHISARNPKLFWVSAAAPLTSVIISTIISFVSKAHGISVIGDLPKGLNPPSANMLTFSGSYVGLALNTGIMTGILSLTEGIAVGRTFASINNYQVDGNKEMMAIGVMNMAGSCASCYVTTGSFSRSAVNYSAGCKTAVSNIVMASAVLVTLLFLMPLFHYTPNVILSAIIITAVIGLIDVRGAARLWKVDKLDFLACMAAFLGVLLVSVQMGLAIAVGISLFKILLQVTRPNMVVKGVVPGTASYRSMAQYREAMRVPSFLVVGVESAIYFANSMYLGERIMRFLREEDERAAKCNQCPVRCIILDMSAVAAIDTSGLDALAELKKVLEKRNIELVLANPVGSVTERLYNSVVGKTFGSDRVFFSVAEAVAAAPHKTQP

Source

organism	Oryza sativa subsp. indica
common_name	long-grained rice
ncbi_taxonomy_id	39946
host_organism	Insect cell expression vector pTIE1

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 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	2.77 Å
resolution_method	—
num_particles	314767

fit	/app/data/saxs_computation/u9/9u9f/9u9f.fit
pddf	/app/data/pr_computation/u9/9u9f/9u9f.pr.out
profile	/app/data/saxs_computation/u9/9u9f/9u9f.dat