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9qk5

X-ray crystal structure of SlPYL1-Caffeic Acid complex

Method: X-RAY DIFFRACTION D_max: 57.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qk5
deposition_date	2025-03-19
last_revision	2025-07-02
title	X-ray crystal structure of SlPYL1-Caffeic Acid complex
keywords	ABA receptor, SlPYL1, Caffeic Acid, 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	17.85 Å
rg_electron	16.57 Å
i0	9289140.00
molecular_weight	21884.0 kDa
excluded_volume	27166 Å³
envelope_volume	31578 Å³
shell_volume	15997 Å³
envelope_diameter	59.4 Å
shell_rg	22.65 Å
envelope_rg	17.09 Å
shape_rg	16.56 Å
total_rg	17.60 Å
total_atoms	1541
n_residues	193
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	57.6 Å
rg_real	17.75 Å
rg_real_error	0.39 Å
i0_real	9.2890e+06
i0_real_error	1.2280e+05
rg_reciprocal	17.77 Å
i0_reciprocal	9289000.0000
total_estimate	0.8087
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	22.6 Å
skewness	0.213
kurtosis	-0.320
angular_range	— – 0.4450 Å⁻¹
current_alpha	0.0000
highest_alpha	1992000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	SlPYL1-NIO
formula_weight	25738.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1683

MDNKPETSLDNPVHQRSEPGSETGSSLSTITTHHLTVPPGLTPEEFQELSSSIAEFHSYRINPGQCSSLLAQRIHAPVETVWTVVRRFDKPQTYKHFIKSCSVGEDFRMTVGSTRDVTVISGLPAATSTERLDILDDDRHVTGFSIIGGEHRLRNYRSVTTVHGFERDGEIWTVVLESYVVDVPEGNTEEDTRLFADTVVKLNLQKLASVTETLAREAGNGSVNSRDASHRS

Source

organism	Solanum lycopersicum
common_name	tomato
ncbi_taxonomy_id	4081
host_organism	Escherichia coli

Entity 2 non-polymer

description	CAFFEIC ACID
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	130

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6. Citations (1)

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length_a	90.066 Å
length_b	90.066 Å
length_c	51.402 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	1.450 Å
resolution_low	33.870 Å
r_factor	0.1963
r_work	0.1955
r_free	0.2132

fit	/app/data/saxs_computation/qk/9qk5/9qk5.fit
pddf	/app/data/pr_computation/qk/9qk5/9qk5.pr.out
profile	/app/data/saxs_computation/qk/9qk5/9qk5.dat