3WHN

Hemerythrin-like domain of DcrH I119H mutant (met)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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) 50: 3421-3423

  • DOI: https://doi.org/10.1039/c3cc48108e
  • Primary Citation of Related Structures:  
    3WHN

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemerythrin-like domain protein DcrH
A, B
136Nitratidesulfovibrio vulgaris str. HildenboroughMutation(s): 1 
Gene Names: dcrH
UniProt
Find proteins for Q726F3 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore Q726F3 
Go to UniProtKB:  Q726F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ726F3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • 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
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SPACEdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-26
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description