SAXSdb — 9vbd

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1. Structure Basics

entry_id	9vbd
deposition_date	2025-06-04
title	Cryo-EM structure of CARD1 ectodomain
keywords	leucine-rich repeat receptor-like kinase, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON MICROSCOPY

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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	26.32 Å
rg_electron	25.09 Å
i0	57034000.00
molecular_weight	60292.0 kDa
excluded_volume	76057 Å³
envelope_volume	90982 Å³
shell_volume	29990 Å³
envelope_diameter	87.5 Å
shell_rg	32.64 Å
envelope_rg	25.35 Å
shape_rg	25.06 Å
total_rg	26.05 Å
total_atoms	4243
n_residues	521
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	84.9 Å
rg_real	26.29 Å
rg_real_error	0.50 Å
i0_real	5.7030e+07
i0_real_error	7.2540e+05
rg_reciprocal	26.30 Å
i0_reciprocal	57030000.0000
total_estimate	0.8951
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.3 Å
skewness	0.329
kurtosis	-0.348
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	17940000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Leucine-rich repeat receptor protein kinase HPCA1,Maltose/maltodextrin-binding periplasmic protein
formula_weight	98137.2 kDa
ec_number	2.7.11.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4243

LTNGLDASALNALKSEWTTPPDGWEGSDPCGTNWVGITCQNDRVVSISLGNLDLEGKLPADISFLSELRILDLSYNPKLSGPLPPNIGNLGKLRNLILVGCSFSGQIPESIGTLKELIYLSLNLNKFSGTIPPSIGLLSKLYWFDIADNQIEGELPVSNGTSAPGLDMLLQTKHFHFGKNKLSGNIPKELFSSNMSLIHVLFDGNQFTGEIPETLSLVKTLTVLRLDRNKLIGDIPSYLNNLTNLNELYLANNRFTGTLPNLTSLTSLYTLDVSNNTLDFSPIPSWISSLPSLSTLRMEGIQLNGPIPISFFSPPQLQTVILKRNSIVESLDFGTDVSSQLEFVDLQYNEITDYKPSANKVLQVILANNPVCLEAGNGPSYCSAIQHNTSFSTLPTNCSPCEPGMEASPTCRCAYPFMGTLYFRSPSFSGLFNSTNFSILQKAIADFFKKFNYPVDSVGVRNIRENPTDHQLLIDLLVFPLGRESFNQTGMSLVGFAFSNQTYKPPPIFGPYIFKADLYKQFSGSAMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQT

Source

organism	Escherichia coli K12
ncbi_taxonomy_id	83333
host_organism	Nicotiana benthamiana

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	4

Entity 3 branched

description	;beta-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 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.26 Å
resolution_method	—
num_particles	130138

fit	/app/data/saxs_computation/vb/9vbd/9vbd.fit
pddf	/app/data/pr_computation/vb/9vbd/9vbd.pr.out
profile	/app/data/saxs_computation/vb/9vbd/9vbd.dat

Cryo-EM structure of CARD1 ectodomain

SAXS Profile

P(r) Distribution