SAXSdb — 2f6c

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

Pyranose 2-oxidase

Peniophora sp. SG

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 TETRAETHYLENE GLYCOL × 4 DI(HYDROXYETHYL)ETHER × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P2OX_PENSG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–595； UniProt 29–623

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	2f6c
Deposition date deposition_date	2005-11-29
Structure title title	Reaction geometry and thermostability of pyranose 2-oxidase from the white-rot fungus Peniophora sp., Thermostability mutant E542K
Keywords keywords	;Flavoprotein, covalent, histidine-bound, lignin degradation, thermostability mutation, D2 tetramer, PHBH fold, GMC oxidoreductase, glutathione-reductase related fold, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

2f6c__assembly_1__model_1

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

Download this curve (.dat)

2f6c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2f6c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.20 Å
Rg (electron density)	39.50 Å
Total Rg	39.89 Å
Atom count	18488
Residues	2308
Excluded volume	326260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2f6c__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 (5)

Entity 1 Entity 1 polymer

Description description	Pyranose 2-oxidase
Molecular weight formula_weight	66512.7 kDa
EC 编号 ec_number	1.1.3.10
Mutation mutation	E542K
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5217

SLPPLPGPDKKVPGMDIKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTHWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLAEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPTNPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMKPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPFTSEAQ

Source Source

Source organism organism	Peniophora sp. SG
NCBI taxonomy ID ncbi_taxonomy_id	204723
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	595

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2f6ca1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

Domain ID domain_id	d2f6ca2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
Family Family family	d.16.1.1 — GMC oxidoreductases

CATH v4.4 (1 domains)

Domain ID domain_id	2f6cA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1920 — Phage tail proteins - 2 layer sandwich fold
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	101.931 Å
Unit-cell length b length_b	101.931 Å
Unit-cell length c length_c	118.602 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	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.840 Å
Low-resolution limit resolution_low	76.700 Å
R factor r_factor	0.1518
R_work r_work	0.1500
R_free r_free	0.1864

Reaction geometry and thermostability of pyranose 2-oxidase from the white-rot fungus Peniophora sp., Thermostability mutant E542K

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

Pyranose 2-oxidase

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

2f6c__assembly_1__model_1

2f6c__assembly_1__model_1 | I(q)

2f6c__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Reaction geometry and thermostability of pyranose 2-oxidase from the white-rot fungus Peniophora sp., Thermostability mutant E542K

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

Pyranose 2-oxidase

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

2f6c__assembly_1__model_1

2f6c__assembly_1__model_1 | I(q)

2f6c__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)