← Back to search

9vby

Lectin FRIL from Lablab purpureus with self glycan

Method: ELECTRON MICROSCOPY D_max: 91.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9vby
deposition_date	2025-06-05
title	Lectin FRIL from Lablab purpureus with self glycan
keywords	Flt3 receptor-interacting lectin, carbohydrate binding protein, lectin, glycoprotein, self glycan, FRIL, PLANT PROTEIN; PLANT PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	30.61 Å
rg_electron	29.23 Å
i0	167185000.00
molecular_weight	104350.0 kDa
excluded_volume	130640 Å³
envelope_volume	152360 Å³
shell_volume	42519 Å³
envelope_diameter	94.7 Å
shell_rg	37.59 Å
envelope_rg	29.14 Å
shape_rg	29.19 Å
total_rg	30.05 Å
total_atoms	7380
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

▼

3. P(r) Analysis (GNOM)

dmax	91.1 Å
rg_real	30.39 Å
rg_real_error	0.49 Å
i0_real	1.6720e+08
i0_real_error	2.5760e+06
rg_reciprocal	30.49 Å
i0_reciprocal	167200000.0000
total_estimate	0.9113
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.3 Å
skewness	0.016
kurtosis	-0.686
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	25660000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.966; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.956

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	Flt3 receptor-interacting lectin
formula_weight	28610.4 kDa
mutation	V33L/S195T/A198P
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7385

AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQLTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISYHGGFLGLFPNANTLNNSSTSENQTTTKAASSNVVAVEFDTYLNPDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTTYYPGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTNVAVDLGHHHHHH

Source

organism	Lablab purpureus
common_name	hyacinth bean
ncbi_taxonomy_id	35936
host_organism	Homo sapiens

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose
formula_weight	545.5 kDa
src_method	syn
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	5

▶

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	—

resolution	2.67 Å
resolution_method	—
num_particles	443332

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