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1b5q

A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE OF POLYAMINE OXIDASE

Method: X-RAY DIFFRACTION D_max: 136.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1b5q
deposition_date	1999-01-07
title	A 30 ANGSTROM U-SHAPED CATALYTIC TUNNEL IN THE CRYSTAL STRUCTURE OF POLYAMINE OXIDASE
keywords	FLAVIN-DEPENDENT AMINE OXIDASE, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

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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	42.70 Å
rg_electron	42.49 Å
i0	385763000.00
molecular_weight	161980.0 kDa
excluded_volume	202660 Å³
envelope_volume	270590 Å³
shell_volume	53225 Å³
envelope_diameter	139.3 Å
shell_rg	47.43 Å
envelope_rg	41.69 Å
shape_rg	42.42 Å
total_rg	42.94 Å
total_atoms	11431
n_residues	1383
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	136.5 Å
rg_real	42.72 Å
rg_real_error	1.41 Å
i0_real	3.8580e+08
i0_real_error	8.2960e+06
rg_reciprocal	42.70 Å
i0_reciprocal	385700000.0000
total_estimate	0.8738
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.2 Å
skewness	0.183
kurtosis	-0.880
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	108700000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.877

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	PROTEIN (POLYAMINE OXIDASE)
formula_weight	53698.5 kDa
src_method	nat
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	12059

ATVGPRVIVVGAGMSGISAAKRLSEAGITDLLILEATDHIGGRMHKTNFAGINVELGANWVEGVNGGKMNPIWPIVNSTLKLRNFRSDFDYLAQNVYKEDGGVYDEDYVQKRIELADSVEEMGEKLSATLHASGRDDMSILAMQRLNEHQPNGPATPVDMVVDYYKFDYEFAEPPRVTSLQNTVPLATFSDFGDDVYFVADQRGYEAVVYYLAGQYLKTDDKSGKIVDPRLQLNKVVREIKYSPGGVTVKTEDNSVYSADYVMVSASLGVLQSDLIQFKPKLPTWKVRAIYQFDMAVYTKIFLKFPRKFWPEGKGREFFLYASSRRGYYGVWQEFEKQYPDANVLLVTVTDEESRRIEQQSDEQTKAEIMQVLRKMFPGKDVPDATDILVPRWWSDRFYKGTFSNWPVGVNRYEYDQLRAPVGRVYFTGEHTSEHYNGYVHGAYLSGIDSAEILINCAQKKMCKYHVQGKYD

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 3 branched

description	;alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	894.8 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	N,N'-BIS(2,3-BUTADIENYL)-1,4-BUTANE-DIAMINE
formula_weight	192.3 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	628

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6. Citations (1)

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length_a	184.600 Å
length_b	184.600 Å
length_c	281.500 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	36

space_group	P 65 2 2
int_tables_number	179
crystal_system	—

resolution	1.900 Å
resolution_low	50.000 Å
r_factor	—
r_work	—
r_free	—

fit	/app/data/saxs_computation/b5/1b5q/1b5q.fit
pddf	/app/data/pr_computation/b5/1b5q/1b5q.pr.out
profile	/app/data/saxs_computation/b5/1b5q/1b5q.dat