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9qrs

Crystal structure of CERK6 extracellular domain

Method: X-RAY DIFFRACTION D_max: 89.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qrs
deposition_date	2025-04-04
last_revision	2025-07-16
title	Crystal structure of CERK6 extracellular domain
keywords	LysM, Chitin, receptor, 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	26.30 Å
rg_electron	25.61 Å
i0	39864400.00
molecular_weight	47419.0 kDa
excluded_volume	58759 Å³
envelope_volume	74535 Å³
shell_volume	25075 Å³
envelope_diameter	95.8 Å
shell_rg	31.70 Å
envelope_rg	25.73 Å
shape_rg	25.60 Å
total_rg	26.36 Å
total_atoms	3328
n_residues	397
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	89.7 Å
rg_real	26.40 Å
rg_real_error	0.71 Å
i0_real	3.9860e+07
i0_real_error	6.1710e+05
rg_reciprocal	26.37 Å
i0_reciprocal	39860000.0000
total_estimate	0.8585
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.9 Å
skewness	0.440
kurtosis	-0.410
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	9961000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.962

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	LysM type receptor kinase
formula_weight	22379.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3705

SKCTHGCALAQASYYLLNGSNLTYISEIMQSSLLTKPEDIVSYNQDTIASKDSVQAGQRINVPFPCDCIEGEFLGHTFQYDVQKGDRYDTIAGTNYANLTTVEWLRRFNSYPPDNIPDTGTLNVTVNCSCGDSGVGDYGLFVTYPLRPGETLGSVASNVKLDSALLQKYNPNVNFNQGSGIVYIPAKDQNGSYVLLGSHHHHHH

Source

organism	Lotus japonicus
ncbi_taxonomy_id	34305
host_organism	Spodoptera frugiperda

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	1

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 4 branched

description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	894.8 kDa
src_method	man
entity_count	1

Entity 5 branched

description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	1

Entity 6 branched

description	beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	366

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6. Citations (1)

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length_a	46.290 Å
length_b	131.580 Å
length_c	53.900 Å
angle_alpha	90.00 °
angle_beta	108.14 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.870 Å
resolution_low	43.990 Å
r_factor	0.1759
r_work	0.1750
r_free	0.1963

fit	/app/data/saxs_computation/qr/9qrs/9qrs.fit
pddf	/app/data/pr_computation/qr/9qrs/9qrs.pr.out
profile	/app/data/saxs_computation/qr/9qrs/9qrs.dat