← Back to search

1dbn

MAACKIA AMURENSIS LEUKOAGGLUTININ (LECTIN) WITH SIALYLLACTOSE

Method: X-RAY DIFFRACTION D_max: 78.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1dbn
deposition_date	1999-11-03
title	MAACKIA AMURENSIS LEUKOAGGLUTININ (LECTIN) WITH SIALYLLACTOSE
keywords	PLANT LECTIN, CARBOHYDRATE BINDING, SIALYLLACTOSE, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	25.15 Å
rg_electron	23.87 Å
i0	47515400.00
molecular_weight	54372.0 kDa
excluded_volume	68176 Å³
envelope_volume	78114 Å³
shell_volume	27211 Å³
envelope_diameter	79.3 Å
shell_rg	31.14 Å
envelope_rg	23.97 Å
shape_rg	23.84 Å
total_rg	24.77 Å
total_atoms	3844
n_residues	478
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	78.0 Å
rg_real	25.10 Å
rg_real_error	0.38 Å
i0_real	4.7520e+07
i0_real_error	6.5860e+05
rg_reciprocal	25.12 Å
i0_reciprocal	47520000.0000
total_estimate	0.9105
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.244
kurtosis	-0.581
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	8402000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.993

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	PROTEIN (LEUKOAGGLUTININ)
formula_weight	25987.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3874

SDELSFTINNFVPNEADLLFQGEASVSSTGVLQLTKVENGQPQKYSVGRALYAAPVRIWGNTTGSVASFSTSFTFVVKAPNPDITSDGLAFYLAPPDSQIPSGSVSKYLGLFNNSNSDSSNQIVAVEFDTYFAHSYDPWDPNYRHIGIDVNGIESIKTVQWDWINGGVAFATITYLAPNKTLIASLVYPSNQTTFSVAASVDLKEILPEWVRVGFSAATGYPTEVETHDVLSWSFTSTL

Entity 2 branched

description	N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose
formula_weight	633.6 kDa
src_method	man
entity_count	2

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	5

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	30

▶

6. Citations (3)

▶

length_a	80.742 Å
length_b	88.450 Å
length_c	84.496 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.750 Å
resolution_low	30.000 Å
r_factor	0.2240
r_work	0.2210
r_free	0.2530

fit	/app/data/saxs_computation/db/1dbn/1dbn.fit
pddf	/app/data/pr_computation/db/1dbn/1dbn.pr.out
profile	/app/data/saxs_computation/db/1dbn/1dbn.dat