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1agm

Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution

Method: X-RAY DIFFRACTION D_max: 68.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1agm
deposition_date	1994-05-13
title	Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution
keywords	HYDROLASE; HYDROLASE
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	22.50 Å
rg_electron	21.32 Å
i0	52314500.00
molecular_weight	54958.0 kDa
excluded_volume	67877 Å³
envelope_volume	75217 Å³
shell_volume	28191 Å³
envelope_diameter	70.3 Å
shell_rg	29.37 Å
envelope_rg	21.55 Å
shape_rg	21.27 Å
total_rg	22.28 Å
total_atoms	3871
n_residues	470
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	68.3 Å
rg_real	22.35 Å
rg_real_error	0.31 Å
i0_real	5.2310e+07
i0_real_error	6.3270e+05
rg_reciprocal	22.38 Å
i0_reciprocal	52320000.0000
total_estimate	0.9017
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.107
kurtosis	-0.468
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	19080000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	GLUCOAMYLASE-471
formula_weight	50450.7 kDa
ec_number	3.2.1.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4461

ATLDSWLSNEATVARTAILNNIGADGAWVSGADSGIVVASPSTDNPDYFYTWTRDSGLVIKTLVDLFRNGDTDLLSTIEHYISSQAIIQGVSNPSGDLSSGGLGEPKFNVDETAYTGSWGRPQRDGPALRATAMIGFGQWLLDNGYTSAATEIVWPLVRNDLSYVAQYWNQTGYDLWEEVNGSSFFTIAVQHRALVEGSAFATAVGSSCSWCDSQAPQILCYLQSFWTGSYILANFDSSRSGKDTNTLLGSIHTFDPEAGCDDSTFQPCSPRALANHKEVVDSFRSIYTLNDGLSDSEAVAVGRYPEDSYYNGNPWFLCTLAAAEQLYDALYQWDKQGSLEITDVSLDFFKALYSGAATGTYSSSSSTYSSIVSAVKTFADGFVSIVETHAASNGSLSEQFDKSDGDELSARDLTWSYAALLTANNRRNSVVPPSWGETSASSVPGTCAATSASGTYSSVTVTSWPSIVA

Source

organism	Aspergillus awamori
ncbi_taxonomy_id	105351

Entity 2 branched

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

Entity 3 branched

description	;alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1397.2 kDa
src_method	man
entity_count	1

Entity 4 branched

description	;4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
formula_weight	645.6 kDa
src_method	man
entity_count	2

Entity 5 non-polymer

description	alpha-D-mannopyranose
formula_weight	180.2 kDa
src_method	man
entity_count	10

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	535

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6. Citations (4)

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length_a	116.700 Å
length_b	103.900 Å
length_c	48.340 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.300 Å
resolution_low	10.000 Å
r_factor	0.1240
r_work	—
r_free	—

fit	/app/data/saxs_computation/ag/1agm/1agm.fit
pddf	/app/data/pr_computation/ag/1agm/1agm.pr.out
profile	/app/data/saxs_computation/ag/1agm/1agm.dat