SAXSdb — 9s9a

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1. Structure Basics

entry_id	9s9a
deposition_date	2025-08-06
title	Crystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with 6-deoxocastasterone.
keywords	receptor kinase, steroid receptor, brassinosteroids, leucine-rich repeat, MEMBRANE PROTEIN; MEMBRANE 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	44.37 Å
rg_electron	44.07 Å
i0	408932000.00
molecular_weight	165390.0 kDa
excluded_volume	206700 Å³
envelope_volume	279520 Å³
shell_volume	55109 Å³
envelope_diameter	153.6 Å
shell_rg	45.83 Å
envelope_rg	43.87 Å
shape_rg	43.98 Å
total_rg	44.45 Å
total_atoms	23055
n_residues	1448
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	152.9 Å
rg_real	44.53 Å
rg_real_error	1.33 Å
i0_real	4.0890e+08
i0_real_error	6.8390e+06
rg_reciprocal	44.37 Å
i0_reciprocal	408900000.0000
total_estimate	0.8681
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.2 Å
skewness	0.394
kurtosis	-0.397
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	38180000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.862

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Receptor-like protein kinase BRI1-like 3
formula_weight	83619.5 kDa
ec_number	2.7.10.1,2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	23142

MKQQWQFLILCLLVLFLTVDSRGRRLLSDDVNDTALLTAFKQTSIKSDPTNFLGNWRYGSGRDPCTWRGVSCSSDGRVIGLDLRNGGLTGTLNLNNLTALSNLRSLYLQGNNFSSGDSSSSSGCSLEVLDLSSNSLTDSSIVDYVFSTCLNLVSVNFSHNKLAGKLKSSPSASNKRITTVDLSNNRFSDEIPETFIADFPNSLKHLDLSGNNVTGDFSRLSFGLCENLTVFSLSQNSISGDRFPVSLSNCKLLETLNLSRNSLIGKIPGDDYWGNFQNLRQLSLAHNLYSGEIPPELSLLCRTLEVLDLSGNSLTGQLPQSFTSCGSLQSLNLGNNKLSGDFLSTVVSKLSRITNLYLPFNNISGSVPISLTNCSNLRVLDLSSNEFTGEVPSGFCSLQSSSVLEKLLIANNYLSGTVPVELGKCKSLKTIDLSFNALTGLIPKEIWTLPKLSDLVMWANNLTGGIPESICVDGGNLETLILNNNLLTGSLPESISKCTNMLWISLSSNLLTGEIPVGIGKLEKLAILQLGNNSLTGNIPSELGNCKNLIWLDLNSNNLTGNLPGELASQAGLVMPGSVSGKQFAFVRNEGGTDCRGAGGLVEFEGIRAERLEHFPMVHSCPKTRIYSGMTMYMFSSNGSMIYLDLSYNAVSGSIPLGYGAMGYLQVLNLGHNLLTGTIPDSFGGLKAIGVLDLSHNDLQGFLPGSLGGLSFLSDLDVSNNNLTGPIPFGGQLTTFPLTRYANNSGLCGVPLPPCSSGSRPTRSHAHPKKAAAENLYFQ

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Trichoplusia ni

Entity 2 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	11

Entity 3 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1721.5 kDa
src_method	man
entity_count	1

Entity 4 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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	1883.7 kDa
src_method	man
entity_count	1

Entity 5 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 6 non-polymer

description	6-deoxocastasterone
formula_weight	450.7 kDa
src_method	man
entity_count	2

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	8

Entity 8 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	62.163 Å
length_b	82.688 Å
length_c	122.196 Å
angle_alpha	107.02 °
angle_beta	91.35 °
angle_gamma	112.46 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.200 Å
resolution_low	48.110 Å
r_factor	0.2236
r_work	0.2205
r_free	0.2803

fit	/app/data/saxs_computation/s9/9s9a/9s9a.fit
pddf	/app/data/pr_computation/s9/9s9a/9s9a.pr.out
profile	/app/data/saxs_computation/s9/9s9a/9s9a.dat

Crystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with 6-deoxocastasterone.

SAXS Profile

P(r) Distribution