4BM0

CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM VII

PDB DOI: https://doi.org/10.2210/pdb4BM0/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271
R-Value Work: 0.228
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain. kehammel@facstaff.wisc.edu.

Macromolecule Content

Total Structure Weight: 35.49 kDa
Atom Count: 2,607
Modelled Residue Count: 329
Deposited Residue Count: 332
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VERSATILE PEROXIDASE I	A	332	Pleurotus ostreatus	Mutation(s): 0 EC: 1.11.1.16
UniProt
Find proteins for Q9UR19 (Pleurotus eryngii) Explore Q9UR19 Go to UniProtKB: Q9UR19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UR19
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 A] MOL2 format, chain D [auth A]	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.271
R-Value Work: 0.228
R-Value Observed: 0.230
Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.7	α = 90
b = 96.7	β = 90
c = 38.4	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Medrano, F.J.

Romero, A.

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2014-12-03
Changes: Data collection
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description