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9vbx

Lectin FRIL from Lablab purpureus complexed to Lewis X tetrasaccharide

Method: ELECTRON MICROSCOPY D_max: 90.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vbx
deposition_date	2025-06-05
title	Lectin FRIL from Lablab purpureus complexed to Lewis X tetrasaccharide
keywords	Flt3 receptor-interacting lectin, carbohydrate binding protein, lectin, glycoprotein, complex type glycan, FRIL, PLANT PROTEIN; PLANT 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	30.57 Å
rg_electron	29.21 Å
i0	169771000.00
molecular_weight	104890.0 kDa
excluded_volume	131230 Å³
envelope_volume	151320 Å³
shell_volume	42272 Å³
envelope_diameter	89.0 Å
shell_rg	37.52 Å
envelope_rg	29.07 Å
shape_rg	29.16 Å
total_rg	30.04 Å
total_atoms	7416
n_residues	924
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	90.1 Å
rg_real	30.35 Å
rg_real_error	0.44 Å
i0_real	1.6980e+08
i0_real_error	2.0420e+06
rg_reciprocal	30.45 Å
i0_reciprocal	169800000.0000
total_estimate	0.9103
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	41.6 Å
skewness	0.001
kurtosis	-0.700
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	24450000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.935

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Flt3 receptor-interacting lectin
formula_weight	27226.9 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7453

AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQLTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNANTLNNSSTSENQTTTKAASSNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTTYYPGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTN

Entity 2 branched

description	alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose
formula_weight	691.6 kDa
src_method	man
entity_count	4

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	37

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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	—

resolution	2.40 Å
resolution_method	—
num_particles	675656

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