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9vbz

Lectin FRIL from Lablab purpureus complexed to oligomannose

Method: ELECTRON MICROSCOPY D_max: 91.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vbz
deposition_date	2025-06-05
title	Lectin FRIL from Lablab purpureus complexed to oligomannose
keywords	;Flt3 receptor-interacting lectin, carbohydrate binding protein, lectin, glycoprotein, high-mannose type glycan. OMS-FRIL, 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	30.68 Å
rg_electron	29.22 Å
i0	169619000.00
molecular_weight	104280.0 kDa
excluded_volume	130260 Å³
envelope_volume	151810 Å³
shell_volume	42325 Å³
envelope_diameter	90.4 Å
shell_rg	37.56 Å
envelope_rg	29.10 Å
shape_rg	29.16 Å
total_rg	30.09 Å
total_atoms	7368
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	91.3 Å
rg_real	30.45 Å
rg_real_error	0.44 Å
i0_real	1.6960e+08
i0_real_error	2.5320e+06
rg_reciprocal	30.55 Å
i0_reciprocal	169600000.0000
total_estimate	0.6507
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	89.5 Å
skewness	-0.000
kurtosis	-0.702
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	27180000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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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	28645.4 kDa
mutation	P145T, Y101S, H102T, S101insertA, G101insertB
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,D,C
atom_count	7398

AQSLSFSFTKFDPNQEDLIFQGHATSTNNVLQLTKLDSAGNPVSSSAGRVLYSAPLRLWEDSAVLTSFDTIINFEISTPYTSRIADGLAFFIAPPDSVISSGSTGGFLGLFPNANTLNNSSTSENQTTTKAASSNVVAVEFDTYLNTDYGDPNYIHIGIDVNSIRSKVTAKWDWQNGKIATAHISYNSVSKRLSVTTYYPGSKPATLSYDIELHTVLPEWVRVGLSASTGQDKERNTVHSWSFTSSLWTNVAVDLGHHHHHH

Source

organism	Lablab purpureus
ncbi_taxonomy_id	35936
host_organism	Homo sapiens

Entity 2 branched

description	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose
formula_weight	504.4 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	30

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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	2.56 Å
resolution_method	—
num_particles	386409

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