SAXSdb — 9vbv

▼

1. Structure Basics

entry_id	9vbv
deposition_date	2025-06-05
title	Cryo-EM structure of a CARD1 ectodomain H197A/H199A/H222A mutant
keywords	leucine-rich repeat receptor-like kinase, SIGNALING PROTEIN; SIGNALING PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.52 Å
rg_electron	25.21 Å
i0	56237300.00
molecular_weight	60030.0 kDa
excluded_volume	75832 Å³
envelope_volume	92138 Å³
shell_volume	30194 Å³
envelope_diameter	87.8 Å
shell_rg	32.85 Å
envelope_rg	25.51 Å
shape_rg	25.17 Å
total_rg	26.20 Å
total_atoms	4227
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

▼

3. P(r) Analysis (GNOM)

dmax	85.4 Å
rg_real	26.48 Å
rg_real_error	0.51 Å
i0_real	5.6240e+07
i0_real_error	7.9530e+05
rg_reciprocal	26.49 Å
i0_reciprocal	56240000.0000
total_estimate	0.8934
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.319
kurtosis	-0.355
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	17500000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.942

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Leucine-rich repeat receptor protein kinase HPCA1,Maltose/maltodextrin-binding periplasmic protein
formula_weight	97936.0 kDa
ec_number	2.7.11.1
mutation	H197A/H199A/H222A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4241

LTNGLDASALNALKSEWTTPPDGWEGSDPCGTNWVGITCQNDRVVSISLGNLDLEGKLPADISFLSELRILDLSYNPKLSGPLPPNIGNLGKLRNLILVGCSFSGQIPESIGTLKELIYLSLNLNKFSGTIPPSIGLLSKLYWFDIADNQIEGELPVSNGTSAPGLDMLLQTKAFAFGKNKLSGNIPKELFSSNMSLIAVLFDGNQFTGEIPETLSLVKTLTVLRLDRNKLIGDIPSYLNNLTNLNELYLANNRFTGTLPNLTSLTSLYTLDVSNNTLDFSPIPSWISSLPSLSTLRMEGIQLNGPIPISFFSPPQLQTVILKRNSIVESLDFGTDVSSQLEFVDLQYNEITDYKPSANKVLQVILANNPVCLEAGNGPSYCSAIQHNTSFSTLPTNCSPCEPGMEASPTCRCAYPFMGTLYFRSPSFSGLFNSTNFSILQKAIADFFKKFNYPVDSVGVRNIRENPTDHQLLIDLLVFPLGRESFNQTGMSLVGFAFSNQTYKPPPIFGPYIFKADLYKQFSGSAMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQT

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

▶

6. Citations (1)

▶

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	3.61 Å
resolution_method	—
num_particles	220439

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

Cryo-EM structure of a CARD1 ectodomain H197A/H199A/H222A mutant

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

EM 3D