3VXJ | pdb_00003vxj

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

• PDB DOI: https://doi.org/10.2210/pdb3VXJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bjerkandera adusta
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2012-09-14 Released: 2012-11-07 
• Deposition Author(s): Sugano, Y., Yoshida, T., Tsuge, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.195 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

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

Sugano, Y., Yoshida, T., Tsuge, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.72 kDa 
• Atom Count: 3,579 
• Modeled Residue Count: 438 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DyP	A	442	Bjerkandera adusta	Mutation(s): 0  Gene Names: dyp EC: 1.11.1.19
UniProt
Find proteins for Q8WZK8 (Bjerkandera adusta) Explore Q8WZK8  Go to UniProtKB:  Q8WZK8
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
3DM	D [auth A], E [auth A]	2,6-dimethoxyphenol C8 H10 O3 KLIDCXVFHGNTTM-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.195 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.167	α = 90
b = 96.344	β = 106.71
c = 49.778	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): Sugano, Y., Yoshida, T., Tsuge, H.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-06
  Changes: Structure summary