5IKG

Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase

• PDB DOI: https://doi.org/10.2210/pdb5IKG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Auricularia auricula-judae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-03-03 Released: 2016-07-13 
• Deposition Author(s): Romero, A., Davo-Siguero, I., Martinez, A.T.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Starting Model: experimental

Literature

Asymmetric sulfoxidation by engineering the heme pocket of a dye-decolorizing peroxidase

Linde, D., Canellas, M., Davo-Siguero, I., Romero, A., Lucas, F., Ruiz-Duenas, F.J., Guallar, V., Martinez, A.T.

(2016) Catal Sci Technol 6: 6277-6285

• DOI: https://doi.org/10.1039/c6cy00539j

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: 47.28 kDa 
• Atom Count: 3,468 
• Modelled Residue Count: 445 
• Deposited Residue Count: 445 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dye-decolorizing peroxidase	A	445	Auricularia auricula-judae	Mutation(s): 1  Gene Names: dyp1 EC: 1.11.1.19
UniProt
Find proteins for I2DBY1 (Auricularia auricula-judae) Explore I2DBY1  Go to UniProtKB:  I2DBY1

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.230 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.887	α = 90
b = 60.985	β = 94.98
c = 81.035	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-13 
Deposition Author(s): Romero, A., Davo-Siguero, I., Martinez, A.T.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2014-55448-P

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2017-12-20
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description