3WHN

Hemerythrin-like domain of DcrH I119H mutant (met)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

H2O2-dependent substrate oxidation by an engineered diiron site in a bacterial hemerythrin

Okamoto, Y.Onoda, A.Sugimoto, H.Takano, Y.Hirota, S.Kurtz Jr., D.M.Shiro, Y.Hayashi, T.

(2014) Chem.Commun.(Camb.) --: --

  • DOI: 10.1039/c3cc48108e

  • PubMed Abstract: 
  • The O2-binding carboxylate-bridged diiron site in DcrH-Hr was engineered in an effort to perform the H2O2-dependent oxidation of external substrates. A His residue was introduced near the diiron site in place of a conserved residue, Ile119. The I119H ...

    The O2-binding carboxylate-bridged diiron site in DcrH-Hr was engineered in an effort to perform the H2O2-dependent oxidation of external substrates. A His residue was introduced near the diiron site in place of a conserved residue, Ile119. The I119H variant promotes the oxidation of guaiacol and 1,4-cyclohexadiene upon addition of H2O2.


    Organizational Affiliation

    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. onoda@chem.eng.osaka-u.ac.jp thayashi@chem.eng.osaka-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hemerythrin-like domain protein DcrH
A, B
136Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 1 
Gene Names: dcrH
Find proteins for Q726F3 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  Q726F3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CFO
Query on CFO

Download SDF File 
Download CCD File 
A, B
CHLORO DIIRON-OXO MOIETY
Cl Fe2 O
KBTPJIQAZMMQJH-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.573α = 92.71
b = 44.082β = 102.59
c = 46.715γ = 90.02
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
HKL-2000data reduction
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling
SPACEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description