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9tdv

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

Method: X-RAY DIFFRACTION D_max: 129.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tdv
deposition_date	2025-11-24
last_revision	2026-02-11
title	Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with raffinose
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	40.17 Å
rg_electron	39.45 Å
i0	931820000.00
molecular_weight	246040.0 kDa
excluded_volume	304590 Å³
envelope_volume	370460 Å³
shell_volume	75196 Å³
envelope_diameter	131.7 Å
shell_rg	47.37 Å
envelope_rg	39.24 Å
shape_rg	39.48 Å
total_rg	39.70 Å
total_atoms	17389
n_residues	2143
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	129.6 Å
rg_real	40.05 Å
rg_real_error	0.84 Å
i0_real	9.3180e+08
i0_real_error	1.3300e+07
rg_reciprocal	40.17 Å
i0_reciprocal	931900000.0000
total_estimate	0.8925
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.8 Å
skewness	0.228
kurtosis	-0.453
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	396400000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.912

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Invertase
formula_weight	62664.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	18504

MRSCPATLCCALQLLAGTCLAQTSANSSSTSPPPAVKTTTTTPAGAYVGPNVTAGRPIVGDYRGQYRPQVHFSPPRHFMNAPNGMFRDDAGTWHLYYQYNPTDIVAGNQHWGHATSSDLYHWVNQPIALYPPRKDVYVFSGSAVVDRNNTSGFFPNQTNGVVAIYTLAEYDSDGSPGPQTQAIAYSHDNGYSFIPYHGNPVIPSDSPQFRDPKVVWHEGHWVMAVAYPHDFAVGIFTSPNLIDWNPTSNFSHHGLLGLQWECPNLVRMPYVDEKGERRDDMWLMVVSINPGAPLGGSVAQYYPGTFNGTHFEAVDAAARIADFGKDSYAGQFFYGSPDDAEDPVFMSWASNWQYTQTVPTADEGWRSAMSLPRRTHLTKSPRVGWKLVTVPYDLSPVMGDALASNDSIANGTITVDFSDVPSNALYWELNVTGLPDSGDISPTATMNFTFSSPVTGEYLRGGMFFGGDSPFFLDRGGTRGFDDVFFTDKVSTNSIVSGASWNMSGILDRSVLELFVNGGIDSATTTFFPTQPLTLAVFGTAGLPEGARVSVRVNALRSAWEGMASEADGLVHGNQS

Source

organism	Komagataella phaffii CBS 7435
ncbi_taxonomy_id	981350
host_organism	Komagataella pastoris

Entity 2 branched

description	alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose
formula_weight	342.3 kDa
src_method	man
entity_count	2

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	4

Entity 4 non-polymer

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

Entity 5 non-polymer

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

Entity 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	16

Entity 7 non-polymer

description	alpha-D-glucopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	alpha-D-galactopyranose
formula_weight	180.2 kDa
src_method	syn
entity_count	2

Entity 9 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1104

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6. Citations (1)

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length_a	79.145 Å
length_b	141.075 Å
length_c	252.710 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	2.000 Å
resolution_low	48.654 Å
r_factor	—
r_work	0.1746
r_free	0.1953

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