SAXSdb — 3vxj

▼

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

DyP

Bjerkandera adusta

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 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2,6-dimethoxyphenol × 2 DIMETHYL SULFOXIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8WZK8_9APHY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–442； UniProt 57–498

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3vxj
Deposition date deposition_date	2012-09-14
Structure title title	Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol
Keywords keywords	DyP, Dye-decolorizing peroxidase, 2, 6-dimethoxyphenol, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3vxj__assembly_1__model_1

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

Download this curve (.dat)

3vxj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vxj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.37 Å
Rg (electron density)	21.33 Å
Total Rg	22.26 Å
Atom count	3414
Residues	438
Excluded volume	60218 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vxj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	DyP
Molecular weight formula_weight	47497.3 kDa
EC 编号 ec_number	1.11.1.19
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	3579

ANDTILPLNNIQGDILVGMKKQKERFVFFQVNDATSFKTALKTYVPERITSAAILISDPSQQPLAFVNLGFSNTGLQALGITDDLGDAQFPDGQFADAANLGDDLSQWVAPFTGTTIHGVFLIGSDQDDFLDQFTDDISSTFGSSITQVQALSGSARPGDQAGHEHFGFLDGISQPSVTGWETTVFPGQAVVPPGIILTGRDGDTGTRPSWALDGSFMAFRHFQQKVPEFNAYTLANAIPANSAGNLTQQEGAEFLGARMFGRWKSGAPIDLAPTADDPALGADPQRNNNFDYSDTLTDETRCPFGAHVRKTNPRQDLGGPVDTFHAMRSSIPYGPETSDAELASGVTAQDRGLLFVEYQSIIGNGFRFQQINWANNANFPFSKPITPGIEPIIGQTTPRTVGGLDPLNQNETFTVPLFVIPKGGEYFFLPSISALTATIAA

Source Source

Source organism organism	Bjerkandera adusta
NCBI taxonomy ID ncbi_taxonomy_id	5331
Host organism host_organism	Aspergillus oryzae

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	1

Entity 3 Entity 3 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	1

Entity 4 Entity 4 non-polymer

Description description	2,6-dimethoxyphenol
Molecular weight formula_weight	154.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	165

▼

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3vxja_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.4 — Dimeric alpha+beta barrel
Family Family family	d.58.4.14 — Dyp-type peroxidase-like

▶

Unit-cell length a length_a	45.167 Å
Unit-cell length b length_b	96.344 Å
Unit-cell length c length_c	49.778 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.390 Å
Low-resolution limit resolution_low	48.170 Å
R factor r_factor	0.1809
R_work r_work	0.1802
R_free r_free	0.1946

Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol

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

DyP

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

3vxj__assembly_1__model_1

3vxj__assembly_1__model_1 | I(q)

3vxj__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)

Dye-decolorizing peroxidase (DyP) complex with 2,6-dimethoxyphenol

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

DyP

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

3vxj__assembly_1__model_1

3vxj__assembly_1__model_1 | I(q)

3vxj__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)