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9ubi

Crystal structure of FERONIA kinase and Ferovicin inhibitor

Method: X-RAY DIFFRACTION D_max: 85.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ubi
deposition_date	2025-04-03
title	Crystal structure of FERONIA kinase and Ferovicin inhibitor
keywords	natural product biosynthetic enzyme, PLANT PROTEIN; PLANT PROTEIN
method	X-RAY DIFFRACTION

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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	26.80 Å
rg_electron	25.81 Å
i0	68969100.00
molecular_weight	65359.0 kDa
excluded_volume	82072 Å³
envelope_volume	99571 Å³
shell_volume	31798 Å³
envelope_diameter	85.1 Å
shell_rg	33.39 Å
envelope_rg	25.87 Å
shape_rg	25.79 Å
total_rg	26.71 Å
total_atoms	4592
n_residues	568
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	85.2 Å
rg_real	26.69 Å
rg_real_error	0.53 Å
i0_real	6.8970e+07
i0_real_error	9.6800e+05
rg_reciprocal	26.72 Å
i0_reciprocal	68970000.0000
total_estimate	0.9022
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	31.8 Å
skewness	0.199
kurtosis	-0.489
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	19300000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.921; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.962

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Receptor-like protein kinase FERONIA
formula_weight	36998.2 kDa
ec_number	2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,A
atom_count	4941

MGSSHHHHHHSSGLEVLFQGPEASSNLCRHFSFAEIKAATKNFDESRVLGVGGFGKVYRGEIDGGTTKVAIKRGNPMSEQGVHEFQTEIEMLSKLRHRHLVSLIGYCEENCEMILVYDYMAHGTMREHLYKTQNPSLPWKQRLEICIGAARGLHYLHTGAKHTIIHRDVKTTNILLDEKWVAKVSDFGLSKTGPTLDHTHVSTVVKGSFGYLDPEYFRRQQLTEKSDVYSFGVVLFEALCARPALNPTLAKEQVSLAEWAPYCYKKGMLDQIVDPYLKGKITPECFKKFAETAMKCVLDQGIERPSMGDVLWNLEFALQLQESAEEN

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	1-[6-(3,5-dichloro-4-hydroxyphenyl)-4-({trans-4-[(dimethylamino)methyl]cyclohexyl}amino)-1,5-naphthyridin-3-yl]ethanone
formula_weight	487.4 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	349

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6. Citations (1)

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length_a	61.794 Å
length_b	83.114 Å
length_c	61.993 Å
angle_alpha	90.00 °
angle_beta	93.38 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.900 Å
resolution_low	49.640 Å
r_factor	0.1722
r_work	0.1714
r_free	0.2026

fit	/app/data/saxs_computation/ub/9ubi/9ubi.fit
pddf	/app/data/pr_computation/ub/9ubi/9ubi.pr.out
profile	/app/data/saxs_computation/ub/9ubi/9ubi.dat

Crystal structure of FERONIA kinase and Ferovicin inhibitor

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

Refinement

Diffraction