4BM2

CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM II

• PDB DOI: https://doi.org/10.2210/pdb4BM2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pleurotus ostreatus
• Expression System: Escherichia coli str. K-12 substr. W3110
• Mutation(s): No 


• Deposited: 2013-05-05 Released: 2014-01-15 
• Deposition Author(s): Medrano, F.J., Romero, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.244 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Literature

Ligninolytic Peroxidase Genes in the Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic and Stability Properties, and Lignin-Degrading Ability.

Fernandez-Fueyo, E., Ruiz-Duenas, F.J., Martinez, M.J., Romero, A., Hammel, K.E., Medrano, F.J., Martinez, A.T.

(2014) Biotechnol Biofuels 7: 2

• PubMed: 24387130 
• DOI: https://doi.org/10.1186/1754-6834-7-2
• Primary Citation of Related Structures:  
  4BLK, 4BLL, 4BLN, 4BLX, 4BLY, 4BLZ, 4BM0, 4BM1, 4BM2, 4BM3, 4BM4


• PubMed Abstract: 
  

  The genome of Pleurotus ostreatus, an important edible mushroom and a model ligninolytic organism of interest in lignocellulose biorefineries due to its ability to delignify agricultural wastes, was sequenced with the purpose of identifying and characterizing the enzymes responsible for lignin degradation.

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Organizational Affiliation: 

Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain. [e-mail].

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: 37.43 kDa 
• Atom Count: 3,099 
• Modelled Residue Count: 337 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANGANESE PEROXIDASE 4	A	338	Pleurotus ostreatus	Mutation(s): 0  EC: 1.11.1.13
UniProt
Find proteins for W5IDB6 (Pleurotus ostreatus) Explore W5IDB6  Go to UniProtKB:  W5IDB6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.244 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.67	α = 90
b = 86.56	β = 107.64
c = 40.03	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-15 
Deposition Author(s): Medrano, F.J., Romero, A.

Revision History  

• Version 1.0: 2014-01-15
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description