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9q84

Crystal structure of Lotus japonicus CHIP13 extracellular domain in complex with chitooctaose

Method: X-RAY DIFFRACTION D_max: 63.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q84
deposition_date	2025-02-21
last_revision	2025-07-16
title	Crystal structure of Lotus japonicus CHIP13 extracellular domain in complex with chitooctaose
keywords	LysM, Chitin, Plant immunity, 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	18.79 Å
rg_electron	17.73 Å
i0	15461600.00
molecular_weight	28764.0 kDa
excluded_volume	35677 Å³
envelope_volume	41072 Å³
shell_volume	19116 Å³
envelope_diameter	69.6 Å
shell_rg	24.42 Å
envelope_rg	18.19 Å
shape_rg	17.70 Å
total_rg	18.83 Å
total_atoms	3900
n_residues	221
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	63.9 Å
rg_real	18.68 Å
rg_real_error	0.34 Å
i0_real	1.5460e+07
i0_real_error	1.7880e+05
rg_reciprocal	18.70 Å
i0_reciprocal	15460000.0000
total_estimate	0.7743
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	25.4 Å
skewness	0.217
kurtosis	-0.168
angular_range	— – 0.4250 Å⁻¹
current_alpha	0.0000
highest_alpha	5977000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.687; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	LysM type receptor kinase
formula_weight	27116.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4243

QQEYLNNNQLDCDNTHNSTYGNVCNSVTSCQSYLTFKSSSPEYNTPSSISYLLNSTPSLVAKSNNITDVTPIITDTMVTVPVTCSCSGGRYQHNATYNLKKTGETYFSIANNTYQSLTTCQALMAQNPYDAKNLFAGDDLHVPLRCACPTKKQSDAGFKYLLTYLVSQGESPDSIAEIFGVDTQSVLDANELDSKSVVFYFTPLLVPLKTEPPARLQIAASPPESPPPAPAGNDSSSSSKKWHHHHHH

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)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1643.6 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	beta-D-mannopyranose-(1-4)-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 5 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	1057.0 kDa
src_method	man
entity_count	1

Entity 6 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	6

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	216

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6. Citations (1)

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length_a	73.882 Å
length_b	66.776 Å
length_c	53.203 Å
angle_alpha	90.00 °
angle_beta	109.35 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.410 Å
resolution_low	48.220 Å
r_factor	0.1482
r_work	0.1464
r_free	0.1814

fit	/app/data/saxs_computation/q8/9q84/9q84.fit
pddf	/app/data/pr_computation/q8/9q84/9q84.pr.out
profile	/app/data/saxs_computation/q8/9q84/9q84.dat