6FKS

Crystal structure of a dye-decolorizing peroxidase from Klebsiella pneumoniae (KpDyP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage.

Pfanzagl, V.Nys, K.Bellei, M.Michlits, H.Mlynek, G.Battistuzzi, G.Djinovic-Carugo, K.Van Doorslaer, S.Furtmuller, P.G.Hofbauer, S.Obinger, C.

(2018) J. Biol. Chem. 293: 14823-14838


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Iron-dependent peroxidase
A
302Klebsiella pneumoniaeMutation(s): 0 
Gene Names: yfeX (yfeX_2, yfeX_3, yfeX_4)
EC: 1.11.1.-
Find proteins for A0A0W8ATM9 (Klebsiella pneumoniae)
Go to UniProtKB:  A0A0W8ATM9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Iron-dependent peroxidase
B
303Klebsiella pneumoniaeMutation(s): 0 
Gene Names: yfeX (yfeX_2, yfeX_3, yfeX_4)
EC: 1.11.1.-
Find proteins for A0A0W8ATM9 (Klebsiella pneumoniae)
Go to UniProtKB:  A0A0W8ATM9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.128 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.520α = 90.00
b = 75.850β = 107.86
c = 75.640γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PHENIXrefinement
PHASERphasing
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaW1224
Austrian Science FundAustriaG005416N

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-15
    Type: Data collection, Database references
  • Version 1.2: 2018-10-03
    Type: Data collection, Database references