3FM4

Crystal Structure Analysis of Fungal Versatile Peroxidase from Pleurotus eryngii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural and Site-directed Mutagenesis Study of Versatile Peroxidase Oxidizing both Mn(II) and Aromatic Substrates

Piontek, K.Choinowski, T.Perez-Boada, M.Ruiz-Duenas, F.J.Martinez, M.J.Plattner, D.A.Martinez, A.T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Versatile peroxidase VPL2331Pleurotus eryngiiMutation(s): 1 
Gene Names: VPL2
EC: 1.11.1.16
UniProt
Find proteins for O94753 (Pleurotus eryngii)
Explore O94753 
Go to UniProtKB:  O94753
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94753
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
CAC
Query on CAC

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN
Query on ZN

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E [auth A]
F [auth A]
G [auth A]
I [auth A]
J [auth A]
E [auth A],
F [auth A],
G [auth A],
I [auth A],
J [auth A],
K [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
H [auth A],
L [auth A]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.144 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.794α = 90
b = 62.794β = 90
c = 97.875γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description