9tdv

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

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Invertase

Komagataella phaffii CBS 7435

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 4 其他Polymer 6	alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose × 2 ;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 ; × 4 beta-D-fructofuranose × 4 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 alpha-D-glucopyranose × 2 alpha-D-galactopyranose × 2 SULFATE ION × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A179H0Q0_PURLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–576； UniProt 1–576 Author chain B； PDBConstruct 1–576； UniProt 1–576 Author chain C； PDBConstruct 1–576； UniProt 1–576 Author chain D； PDBConstruct 1–576； UniProt 1–576

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9tdv
Deposition date deposition_date	2025-11-24
Last revision last_revision	2026-02-11
Structure title title	Structure of D81A-Fructofuranosidase from Purpureocilum lilacinum in complex with raffinose
Keywords keywords	Fructooligosaccharides Glycosyl hydrolase Beta-fructofuranosidase Family GH32 Transfructosylation, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9tdv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9tdv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9tdv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.17 Å
Rg (electron density)	39.45 Å
Total Rg	39.70 Å
Atom count	17389
Residues	2143
Excluded volume	304590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9tdv__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	Invertase
Molecular weight formula_weight	62664.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	18504

MRSCPATLCCALQLLAGTCLAQTSANSSSTSPPPAVKTTTTTPAGAYVGPNVTAGRPIVGDYRGQYRPQVHFSPPRHFMNAPNGMFRDDAGTWHLYYQYNPTDIVAGNQHWGHATSSDLYHWVNQPIALYPPRKDVYVFSGSAVVDRNNTSGFFPNQTNGVVAIYTLAEYDSDGSPGPQTQAIAYSHDNGYSFIPYHGNPVIPSDSPQFRDPKVVWHEGHWVMAVAYPHDFAVGIFTSPNLIDWNPTSNFSHHGLLGLQWECPNLVRMPYVDEKGERRDDMWLMVVSINPGAPLGGSVAQYYPGTFNGTHFEAVDAAARIADFGKDSYAGQFFYGSPDDAEDPVFMSWASNWQYTQTVPTADEGWRSAMSLPRRTHLTKSPRVGWKLVTVPYDLSPVMGDALASNDSIANGTITVDFSDVPSNALYWELNVTGLPDSGDISPTATMNFTFSSPVTGEYLRGGMFFGGDSPFFLDRGGTRGFDDVFFTDKVSTNSIVSGASWNMSGILDRSVLELFVNGGIDSATTTFFPTQPLTLAVFGTAGLPEGARVSVRVNALRSAWEGMASEADGLVHGNQS

Source Source

Source organism organism	Komagataella phaffii CBS 7435
NCBI taxonomy ID ncbi_taxonomy_id	981350
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 branched

Description description	alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description 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 ;
Molecular weight formula_weight	1397.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	beta-D-fructofuranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 7 Entity 7 non-polymer

Description description	alpha-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	alpha-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1104

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Unit-cell length a length_a	79.145 Å
Unit-cell length b length_b	141.075 Å
Unit-cell length c length_c	252.710 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	48.654 Å
R factor r_factor	—
R_work r_work	0.1746
R_free r_free	0.1953

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Invertase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9tdv__assembly_1__model_1

9tdv__assembly_1__model_1 | I(q)

9tdv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Invertase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9tdv__assembly_1__model_1

9tdv__assembly_1__model_1 | I(q)

9tdv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

7. Citations (1)