SAXSdb — 1abr

▼

1. Structure Basics

entry_id	1abr
deposition_date	1994-11-11
title	CRYSTAL STRUCTURE OF ABRIN-A
keywords	;GLYCOSIDASE-CARBOHYDRATE complex, LECTIN, LECTIN (AGGLUTININ), GLYCOPROTEIN, PLANT SEED PROTEIN, PLANT TOXIN, PROTEIN SYNTHESIS INHIBITOR, TOXIN ;; GLYCOSIDASE/CARBOHYDRATE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	26.15 Å
rg_electron	25.13 Å
i0	62640100.00
molecular_weight	59970.0 kDa
excluded_volume	74290 Å³
envelope_volume	88267 Å³
shell_volume	29505 Å³
envelope_diameter	85.8 Å
shell_rg	32.24 Å
envelope_rg	25.09 Å
shape_rg	25.13 Å
total_rg	25.85 Å
total_atoms	5198
n_residues	518
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	83.1 Å
rg_real	26.13 Å
rg_real_error	0.54 Å
i0_real	6.2640e+07
i0_real_error	9.2610e+05
rg_reciprocal	26.14 Å
i0_reciprocal	62640000.0000
total_estimate	0.9006
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	28.6 Å
skewness	0.329
kurtosis	-0.417
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	12510000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.954

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	ABRIN-A
formula_weight	28124.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5798

EDRPIKFSTEGATSQSYKQFIEALRERLRGGLIHDIPVLPDPTTLQERNRYITVELSNSDTESIEVGIDVTNAYVVAYRAGTQSYFLRDAPSSASDYLFTGTDQHSLPFYGTYGDLERWAHQSRQQIPLGLQALTHGISFFRSGGNDNEEKARTLIVIIQMVAEAARFRYISNRVRVSIQTGTAFQPDAAMISLENNWDNLSRGVQESVQDTFPNQVTLTNIRNEPVIVDSLSHPTVAVLALMLFVCNPPN

Source

organism	Abrus precatorius
common_name	Indian licorice
ncbi_taxonomy_id	3816

Entity 2 polymer

description	ABRIN-A
formula_weight	30111.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

IVEKSKICSSRYEPTVRIGGRDGMCVDVYDNGYHNGNRIIMWKCKDRLEENQLWTLKSDKTIRSNGKCLTTYGYAPGSYVMIYDCTSAVAEATYWEIWDNGTIINPKSALVLSAESSSMGGTLTVQTNEYLMRQGWRTGNNTSPFVTSISGYSDLCMQAQGSNVWMADCDSNKKEQQWALYTDGSIRSVQNTNNCLTSKDHKQGSTILLMGCSNGWASQRWVFKNDGSIYSLYDDMVMDVKGSDPSLKQIILWPYTGKPNQIWLTLF

Entity 3 branched

description	;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-L-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	1

Entity 4 branched

description	;beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	200

▶

6. Citations (4)

▶

length_a	84.580 Å
length_b	73.070 Å
length_c	48.230 Å
angle_alpha	90.00 °
angle_beta	96.20 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.140 Å
resolution_low	10.000 Å
r_factor	0.1890
r_work	0.1890
r_free	—

fit	/app/data/saxs_computation/ab/1abr/1abr.fit
pddf	/app/data/pr_computation/ab/1abr/1abr.pr.out
profile	/app/data/saxs_computation/ab/1abr/1abr.dat

CRYSTAL STRUCTURE OF ABRIN-A

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

Refinement

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 branched

Entity 5 water

6. Citations (4)

7. Files & Curves (10)

Files (7)

Curves (3)