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9vxi

Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)

Method: ELECTRON MICROSCOPY D_max: 110.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vxi
deposition_date	2025-07-18
title	Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)
keywords	Chloroplast; Plastoquinone-9; Catalysis, TRANSFERASE; TRANSFERASE
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	35.51 Å
rg_electron	34.95 Å
i0	204465000.00
molecular_weight	116780.0 kDa
excluded_volume	146970 Å³
envelope_volume	181320 Å³
shell_volume	44365 Å³
envelope_diameter	118.5 Å
shell_rg	40.49 Å
envelope_rg	34.70 Å
shape_rg	34.98 Å
total_rg	35.25 Å
total_atoms	8190
n_residues	1044
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	110.6 Å
rg_real	35.42 Å
rg_real_error	0.72 Å
i0_real	2.0450e+08
i0_real_error	3.3820e+06
rg_reciprocal	35.48 Å
i0_reciprocal	204500000.0000
total_estimate	0.9063
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	44.3 Å
skewness	0.158
kurtosis	-0.670
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	33220000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.895

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Probable solanesyl-diphosphate synthase 3, chloroplastic
formula_weight	35721.6 kDa
ec_number	2.5.1.84
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	8190

MSVSSLLEVVADDLLKLNNNLKSLVGAENPVLVSAAEQIFGAGGKRLRPALVFLVSRATAELAGLLELTTEHQRLAEIIEMIHTASLIHDDVIDDSGMRRGKETIHQLYGTRVAVLAGDFMFAQSSWFLANLENIEVIKLISQVIKDFASGEIKQASTLFDCDITLDDYLLKSYYKTASLIAASTRSAAIFSGVSTAICEQMYEYGRNLGLSFQVVDDILDFTQSAEQLGKPAGSDLAKGNLTAPVIFALQDEPQLREIIDSEFSETNSLATAIELVHRSGGIKRAHELAREKGEIAIQSLQCLPRSEFRSTLENMVKYNLERID

Source

organism	Oryza sativa Japonica Group
common_name	Japanese rice
ncbi_taxonomy_id	39947
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Fibrillin protein 5 homolog
formula_weight	22165.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

EAALGDAKDALYAALEGMNRGIFGMTSEKRSEIHALVELLESKNPTPEPTDKLQDKVDGCWRLVYSTISILGKKRTKLGLRDFISLGDFFQMIDVKEEKAVNVIKFSARALKILSGQLTIEASYKITTKTKVDITLDSSTITPDQLMNIFQKNYDMLLAIFNPEGWLEITYVDESLRIGRDDKANIFVLERADPSEV

Source

organism	Oryza sativa Japonica Group
common_name	Japanese rice
ncbi_taxonomy_id	39947
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	phosphonooxy-[(10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenyl]sulfanyl-phosphinic acid
formula_weight	466.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	COBALT (II) ION
formula_weight	58.9 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	2.47 Å
resolution_method	—
num_particles	577732

fit	/app/data/saxs_computation/vx/9vxi/9vxi.fit
pddf	/app/data/pr_computation/vx/9vxi/9vxi.pr.out
profile	/app/data/saxs_computation/vx/9vxi/9vxi.dat

Cryo-EM structure of the SPS3-FBN5 complex from Oryza sativa in complex with cobalt and geranylgeranyl S-thiodiphosphate (GGSPP)

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)