SAXSdb — 5oxt

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

UNSPECIFIC PEROXYGENASE

Agrocybe aegerita

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 MAGNESIUM ION × 1 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ACETATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 MAGNESIUM ION × 1 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ACETATE ION × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	PROTOPORPHYRIN IX CONTAINING FE × 1 MAGNESIUM ION × 1 CHLORIDE ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ACETATE ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APO1_AGRAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–328； UniProt 44–371 Author chain B； PDBConstruct 1–328； UniProt 44–371 Author chain C； PDBConstruct 1–328； UniProt 44–371

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	5oxt
Deposition date deposition_date	2017-09-07
Structure title title	DIRECT-EVOLUTIONED UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA, IN COMPLEX WITH ACETATE
Keywords keywords	directed evolution, PaDaI, unspecific peroxygenase, UPO, heme-thiolate peroxidase, Agrocybe aegerita, acetate, 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.

5oxt__assembly_1__model_1

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

Download this curve (.dat)

5oxt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5oxt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.10 Å
Rg (electron density)	19.10 Å
Total Rg	20.07 Å
Atom count	2653
Residues	327
Excluded volume	46700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5oxt__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5oxt__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5oxt__assembly_3__model_1`	monomeric （1）	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 (7)

Entity 1 Entity 1 polymer

Description description	UNSPECIFIC PEROXYGENASE
Molecular weight formula_weight	35947.9 kDa
EC 编号 ec_number	1.11.2.1
Mutation mutation	V57A, L67F, V75I, I248V, F311L
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9345

EPGLPPGPLENSSAKLVNDEAHPWKPLRPGDIRGPCPGLNTLASHGYLPRNGVATPAQIINAVQEGFNFDNQAAIFATYAAHLVDGNLITDLLSIGRKTRLTGPDPPPPASVGGLNEHGTFEGDASMTRGDAFFGNNHDFNETLFEQLVDYSNRFGGGKYNLTVAGELRFKRIQDSIATNPNFSFVDFRFFTAYGETTFPANLFVDGRRDDGQLDMDAARSFFQFSRMPDDFFRAPSPRSGTGVEVVVQAHPMQPGRNVGKINSYTVDPTSSDFSTPCLMYEKFVNITVKSLYPNPTVQLRKALNTNLDFLFQGVAAGCTQVFPYGRD

Source Source

Source organism organism	Agrocybe aegerita
Common name common_name	Black poplar mushroom
NCBI taxonomy ID ncbi_taxonomy_id	5400
Host organism host_organism	Komagataella phaffii CBS 7435

Entity 2 Entity 2 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	13

Entity 6 Entity 6 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1282

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5oxtA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	489 — Chloroperoxidase
Homologous superfamily homologous superfamily	10 — Chloroperoxidase-like

Domain ID domain_id	5oxtB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	489 — Chloroperoxidase
Homologous superfamily homologous superfamily	10 — Chloroperoxidase-like

Domain ID domain_id	5oxtC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	489 — Chloroperoxidase
Homologous superfamily homologous superfamily	10 — Chloroperoxidase-like

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Unit-cell length a length_a	64.999 Å
Unit-cell length b length_b	99.151 Å
Unit-cell length c length_c	83.890 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	1.420 Å
Low-resolution limit resolution_low	45.230 Å
R factor r_factor	0.1510
R_work r_work	0.1503
R_free r_free	0.1642

DIRECT-EVOLUTIONED UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA, IN COMPLEX WITH ACETATE

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

UNSPECIFIC PEROXYGENASE

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

5oxt__assembly_1__model_1

5oxt__assembly_1__model_1 | I(q)

5oxt__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

DIRECT-EVOLUTIONED UNSPECIFIC PEROXYGENASE FROM AGROCYBE AEGERITA, IN COMPLEX WITH ACETATE

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

UNSPECIFIC PEROXYGENASE

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

5oxt__assembly_1__model_1

5oxt__assembly_1__model_1 | I(q)

5oxt__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)