2ign

Crystal structure of recombinant pyranose 2-oxidase H167A mutant

Method: X-RAY DIFFRACTION

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

Pyranose oxidase

Trametes ochracea

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 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 water × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	FLAVIN-ADENINE DINUCLEOTIDE × 4 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7ZA32_TRAOC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–623； UniProt 1–623 Author chain B； PDBConstruct 1–623； UniProt 1–623 Author chain C； PDBConstruct 1–623； UniProt 1–623 Author chain D； PDBConstruct 1–623； UniProt 1–623 Author chain E； PDBConstruct 1–623； UniProt 1–623 Author chain F； PDBConstruct 1–623； UniProt 1–623 Author chain G； PDBConstruct 1–623； UniProt 1–623 Author chain H； PDBConstruct 1–623； UniProt 1–623

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	2ign
Deposition date deposition_date	2006-09-22
Structure title title	Crystal structure of recombinant pyranose 2-oxidase H167A mutant
Keywords keywords	OXIDOREDUCTASE, GMC OXIDOREDUCTASE, H167A MUTANT, ROSSMANN FOLD, PHBH FOLD, HOMOTETRAMER, 8-ALPHA-(N3) HISTIDYL FLAVINYLATION; 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.

2ign__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ign__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ign__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	40.25 Å
Rg (electron density)	39.59 Å
Total Rg	39.94 Å
Atom count	18436
Residues	2308
Excluded volume	325110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ign__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ign__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Pyranose oxidase
Molecular weight formula_weight	69346.7 kDa
EC 编号 ec_number	1.1.3.10
Mutation mutation	H167A
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,C,E,F,H,G
Atom count atom_count	41758

MSTSSSDPFFNFAKSSFRSAAAQKASASSLPPLPGPDKKVPGMDIKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTAWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLTEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPANPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPFTSEAQ

Source Source

Source organism organism	Trametes ochracea
NCBI taxonomy ID ncbi_taxonomy_id	230624
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	8

Entity 3 Entity 3 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4758

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2igna1
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	d2igna2
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

Domain ID domain_id	d2ignb1
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	d2ignb2
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

Domain ID domain_id	d2ignc1
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	d2ignc2
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

Domain ID domain_id	d2ignd1
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	d2ignd2
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

Domain ID domain_id	d2igne1
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	d2igne2
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

Domain ID domain_id	d2ignf1
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	d2ignf2
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

Domain ID domain_id	d2igng1
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	d2igng2
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

Domain ID domain_id	d2ignh1
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	d2ignh2
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 (8 domains)

Domain ID domain_id	2ignA02
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 —

Domain ID domain_id	2ignB02
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 —

Domain ID domain_id	2ignC02
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 —

Domain ID domain_id	2ignD02
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 —

Domain ID domain_id	2ignE02
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 —

Domain ID domain_id	2ignF02
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 —

Domain ID domain_id	2ignG02
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 —

Domain ID domain_id	2ignH02
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	168.066 Å
Unit-cell length b length_b	102.996 Å
Unit-cell length c length_c	168.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	39.000 Å
R factor r_factor	0.1722
R_work r_work	0.1719
R_free r_free	0.2053

Crystal structure of recombinant pyranose 2-oxidase H167A mutant

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

Pyranose 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

2ign__assembly_2__model_1

2ign__assembly_2__model_1 | I(q)

2ign__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of recombinant pyranose 2-oxidase H167A mutant

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

Pyranose 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

2ign__assembly_2__model_1

2ign__assembly_2__model_1 | I(q)

2ign__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)