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9tdu

Structure of Fructofuranosidase from Purpureocilum lilacinum

Method: X-RAY DIFFRACTION D_max: 98.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tdu
deposition_date	2025-11-24
last_revision	2026-02-11
title	Structure of Fructofuranosidase from Purpureocilum lilacinum
keywords	Fructooligosaccharides (FOS) 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	31.13 Å
rg_electron	29.94 Å
i0	244929000.00
molecular_weight	122200.0 kDa
excluded_volume	151160 Å³
envelope_volume	179380 Å³
shell_volume	47836 Å³
envelope_diameter	104.4 Å
shell_rg	38.78 Å
envelope_rg	30.04 Å
shape_rg	29.93 Å
total_rg	30.67 Å
total_atoms	8636
n_residues	1069
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	98.0 Å
rg_real	31.00 Å
rg_real_error	0.60 Å
i0_real	2.4490e+08
i0_real_error	4.3480e+06
rg_reciprocal	31.06 Å
i0_reciprocal	244900000.0000
total_estimate	0.8940
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.5 Å
skewness	0.248
kurtosis	-0.388
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	101500000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.912

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Invertase
formula_weight	62621.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9150

MRSCPATLCCALQLLAGTCLAQTSANSSSTSPPPAVKTTTTTPAGAYVGPNVTAGRPIVGDYRGQYRPQVHFSPPRHFMNDPNGMFRDDAGTWHLYYQYNPTDIVAGNQHWGHATSSDLYHWVNQPIALYPPRKDVYVFSGSAVVDRNNTSGFFPNQTNGVVAIYTLAEYDSDGSPGPQTQAIAYSHDNGYSFIPYHGNPVIPSDSPQFRDPKVVWHEGHWVMAVAYPHDFAVGIFTSPNLIDWNPTSNFSHHGLLGLQWECPNLVRMPYVDEKGERRDDMWLMVVSINPGAPLGGSVAQYYPGTFNGTHFEAVDAAARIADFGKDSYAGQFFYGSPDDAEDPVFMSWASNWQYTQTVPTADEGWRSAMSLPRRTHLTKSPRVGWKLVTVPYDLSPVMGDALASNDSIANGTITVDFSDVPSNALYWELNVTGLPDSGDISPTATMNFTFSSPVTGEYLRGGMFFGGDSPFFLDRGGTRGFDDVFFTDKVSTNSIVSGASWNMSGILDRSVLELFVNGGIDSATTTFFPTQPLTLAVFGTAGLPEGARVSVRVNALRSAWEGMASEADGLVHGNQ

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)]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	1559.4 kDa
src_method	man
entity_count	2

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	8

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	514

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6. Citations (1)

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length_a	103.412 Å
length_b	111.693 Å
length_c	219.254 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.100 Å
resolution_low	46.809 Å
r_factor	0.1957
r_work	0.1940
r_free	0.2312

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