6FSL | pdb_00006fsl

F194W mutant of the dye-decolorizing peroxidase (DYP) from Pleurotus ostreatus

PDB DOI: https://doi.org/10.2210/pdb6FSL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pleurotus ostreatus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-02-19 Released: 2019-03-13
Deposition Author(s): Romero, A., Davo-Siguero, I.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.243 (Depositor), 0.240 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of two mutants: F194Y and F194W of the Dye-decolorizing peroxidase DYP from Pleurotus ostreatus

Romero, A., Davo-Siguero, I., Martinez, A.T.

To be published.

Macromolecule Content

Total Structure Weight: 107.48 kDa
Atom Count: 7,766
Modeled Residue Count: 968
Deposited Residue Count: 968
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DyP-type peroxidase	A, B	484	Pleurotus ostreatus	Mutation(s): 1 Gene Names: DyP4, PLEOSDRAFT_1069077
UniProt
Find proteins for A0A067N4E7 (Pleurotus ostreatus (strain PC15)) Explore A0A067N4E7 Go to UniProtKB: A0A067N4E7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A067N4E7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.243 (Depositor), 0.240 (DCC)
R-Value Work: 0.181 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.869	α = 90
b = 118.14	β = 90
c = 133.078	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Davo-Siguero, I.

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

Revision History (Full details and data files)

Version 1.0: 2019-03-13
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.