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9v79

Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa

Method: X-RAY DIFFRACTION D_max: 70.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v79
deposition_date	2025-05-27
title	Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa
keywords	dOsCERK1-KD-AMP-PNP complex, the kinase domain of OsCERK1 bound to AMP-PNP in dephosphorylated state, TRANSFERASE; TRANSFERASE
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	20.02 Å
rg_electron	19.11 Å
i0	13959400.00
molecular_weight	28815.0 kDa
excluded_volume	36431 Å³
envelope_volume	42217 Å³
shell_volume	18855 Å³
envelope_diameter	71.4 Å
shell_rg	25.17 Å
envelope_rg	19.38 Å
shape_rg	19.12 Å
total_rg	19.98 Å
total_atoms	2028
n_residues	252
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	70.4 Å
rg_real	20.03 Å
rg_real_error	0.59 Å
i0_real	1.3960e+07
i0_real_error	1.9720e+05
rg_reciprocal	20.03 Å
i0_reciprocal	13960000.0000
total_estimate	0.8522
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.415
kurtosis	-0.115
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	3868000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.703; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Chitin elicitor receptor kinase 1
formula_weight	33478.2 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2112

GITVDKSVEFSYEELSNATQGFSIGNKIGQGGFGAVYYAELRGEKAAIKKMDMQATHEFLAELKVLTHVHHLNLVRLIGYCIESSLFLVYEFIENGNLSQHLRGMGYEPLSWAARIQIALDSARGLEYIHEHTVPVYIHRDIKSANILIDKNYRAKVADFGLTKLTEVGGTSMPTGTRVVGTFGYMPPEYARYGDVSPKVDVYAFGVVLYELISAKEAIVRSTESSSDSKGLVYLFEEALNSPDPKEGLRTLIDPKLGEDYPIDSILKLTQLAKVCTQEDPKLRPSMRSVVVALMTLSSTSE

Source

organism	Oryza sativa Japonica Group
common_name	Japanese rice
ncbi_taxonomy_id	39947
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	84

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6. Citations (1)

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length_a	58.213 Å
length_b	58.213 Å
length_c	283.132 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.120 Å
resolution_low	50.410 Å
r_factor	0.2380
r_work	0.2338
r_free	0.2754

fit	/app/data/saxs_computation/v7/9v79/9v79.fit
pddf	/app/data/pr_computation/v7/9v79/9v79.pr.out
profile	/app/data/saxs_computation/v7/9v79/9v79.dat

Structural basis of signal activation and transduction by chitin elicitor receptor kinase 1 in Oryza sativa

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