6FSK | pdb_00006fsk

F194Y mutant of the Dye-decolorizing peroxidase (DYP) from Pleurotus ostreatus

• PDB DOI: https://doi.org/10.2210/pdb6FSK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pleurotus ostreatus PC15
• Expression System: Escherichia coli #1/H766
• Mutation(s): Yes 


• Deposited: 2018-02-19 Released: 2018-12-26 
• Deposition Author(s): Romero, A., Davo-Siguero, I.
• Funding Organization(s): Spanish Ministry of Economy and Competitiveness

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Description of a non-canonical Mn(II)-oxidation site in peroxidases

Fernandez-Fueyo, E., Davo-Siguero, I., Almendral, D., Linde, D., Baratto, M.C., Pogni, R., Romero, A., Guallar, V., Martinez, A.T.

(2018) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.8b02306

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 107.71 kDa 
• Atom Count: 8,701 
• Modeled Residue Count: 968 
• Deposited Residue Count: 968 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DyP-type peroxidase	A, B	484	Pleurotus ostreatus PC15	Mutation(s): 1  Gene Names: DyP4, PLEOSDRAFT_1069077
UniProt
Find proteins for A0A067N4E7 (Pleurotus ostreatus (strain PC15)) Explore A0A067N4E7  Go to UniProtKB:  A0A067N4E7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.717	α = 90
b = 117.575	β = 90
c = 140.434	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-26 
Deposition Author(s): Romero, A., Davo-Siguero, I.

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Funding Organization	Location	Grant Number
Spanish Ministry of Economy and Competitiveness	Spain	BFU2016-77835-R

Revision History  

• Version 1.0: 2018-12-26
  Type: Initial release
  
• Version 2.0: 2019-01-23
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary