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9tdx

Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with sucrose

Method: X-RAY DIFFRACTION D_max: 126.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tdx
deposition_date	2025-11-24
last_revision	2026-02-11
title	Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with sucrose
keywords	Fructooligosaccharides Glycosyl hydrolase Beta-fructofuranosidase Family GH32 Transfructosylation, 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	40.14 Å
rg_electron	39.43 Å
i0	929885000.00
molecular_weight	245700.0 kDa
excluded_volume	304170 Å³
envelope_volume	372140 Å³
shell_volume	75454 Å³
envelope_diameter	132.7 Å
shell_rg	47.38 Å
envelope_rg	39.26 Å
shape_rg	39.47 Å
total_rg	39.69 Å
total_atoms	17364
n_residues	2142
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	126.4 Å
rg_real	40.02 Å
rg_real_error	0.68 Å
i0_real	9.2990e+08
i0_real_error	1.5860e+07
rg_reciprocal	40.14 Å
i0_reciprocal	930000000.0000
total_estimate	0.8890
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.6 Å
skewness	0.228
kurtosis	-0.452
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0002
highest_alpha	376200000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.784

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Invertase
formula_weight	62708.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	18328

MRSCPATLCCALQLLAGTCLAQTSANSSSTSPPPAVKTTTTTPAGAYVGPNVTAGRPIVGDYRGQYRPQVHFSPPRHFMNDPNGMFRDDAGTWHLYYQYNPTDIVAGNQHWGHATSSDLYHWVNQPIALYPPRKDVYVFSGSAVVDRNNTSGFFPNQTNGVVAIYTLAEYDSDGSPGPQTQAIAYSHDNGYSFIPYHGNPVIPSDSPQFRDPKVVWHEGHWVMAVAYPHDFAVGIFTSPNLIDWNPTSNFSHHGLLGLQWECPNLVRMPYVDEKGERRDDMWLMVVSINPGAPLGGSVAQYYPGTFNGTHFEAVDAAARIADFGKDSYAGQFFYGSPDDAEDPVFMSWASNWQYTQTVPTADEGWRSAMSLPRRTHLTKSPRVGWKLVTVPYDLSPVMGDALASNDSIANGTITVDFSDVPSNALYWELNVTGLPDSGDISPTATMNFTFSSPVTGEYLRGGMFFGGDSPFFLDRGGTRGFDDVFFTDKVSTNSIVSGASWNMSGILDRSVLELFVNGGIDSATTTFFPTQPLTLAVFGTAGLPEGARVSVRVNALRSAWEGMASEADGLVHGNQS

Source

organism	Komagataella phaffii CBS 7435
ncbi_taxonomy_id	981350
host_organism	Komagataella pastoris

Entity 2 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	4

Entity 3 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	1

Entity 4 non-polymer

description	alpha-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	beta-D-fructofuranose
formula_weight	180.2 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	6

Entity 7 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	15

Entity 9 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	953

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6. Citations (1)

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length_a	79.104 Å
length_b	141.122 Å
length_c	252.658 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.004 Å
resolution_low	49.408 Å
r_factor	—
r_work	0.1792
r_free	0.1977

fit	/app/data/saxs_computation/td/9tdx/9tdx.fit
pddf	/app/data/pr_computation/td/9tdx/9tdx.pr.out
profile	/app/data/saxs_computation/td/9tdx/9tdx.dat