2E2Y | pdb_00002e2y

Crystal Structure of F43W/H64D/V68I Myoglobin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.170 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

This is version 1.3 of the entry. See complete history. 


Literature

Reactivities of oxo and peroxo intermediates studied by hemoprotein mutants

Watanabe, Y., Nakajima, H., Ueno, T.

(2007) Acc Chem Res 40: 554-562

  • DOI: https://doi.org/10.1021/ar600046a
  • Primary Citation of Related Structures:  
    2E2Y

  • PubMed Abstract: 

    A series of myoglobin mutants, in which distal sites are modified by site-directed mutagenesis, are able to catalyze peroxidase, catalase, and P450 reactions even though their proximal histidine ligands are intact. More importantly, reactions of P450, catalase, and peroxidase substrates and compound I of myoglobin mutants can be observed spectroscopically. Thus, detailed oxidation mechanisms were examined. On the basis of these results, we suggest that the different reactivities of P450, catalase, and peroxidase are mainly caused by their active site structures, but not the axial ligand. We have also prepared compound 0 under physiological conditions by employing a mutant of cytochrome c 552. Compound 0 is not able to oxidize ascorbic acid.

    • Organizational Affiliation: 

    Research Center for Materials Science and Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin154Physeter macrocephalusMutation(s): 4 
EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P02185 (Physeter macrocephalus)
Explore P02185 
Go to UniProtKB:  P02185
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02185
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.170 (Depositor) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.651α = 90
b = 90.651β = 90
c = 45.447γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description