7VDN

High resolution crystal structure of Sperm Whale Myoglobin in the carbonmonoxy form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

X-ray fluorescence holography of biological metal sites: Application to myoglobin.

Sato-Tomita, A.Ang, A.K.R.Kimura, K.Marumi, R.Happo, N.Matsushita, T.Park, S.Y.Shibayama, N.Sasaki, Y.C.Hayashi, K.

(2022) Biochem Biophys Res Commun 635: 277-282

  • DOI: https://doi.org/10.1016/j.bbrc.2022.10.003
  • Primary Citation of Related Structures:  
    7VDN

  • PubMed Abstract: 

    X-ray fluorescence holography (XFH) is a relatively new technique capable of providing unique three-dimensional structural information around specific atoms that act as a light source in crystalline samples. So far, XFH has typically been applied to inorganic materials such as dopants in metals and semiconductors. Here, we investigate the possibility of using XFH to visualize the metal active site in sperm whale myoglobin (Mb), a monomeric oxygen storage heme protein. We demonstrate that the atomic images reconstructed from the hologram data of crystals of carbonmonoxy myoglobin (MbCO) are moderately consistent with the crystal structure, which is also determined in this study by X-ray crystallography in the near-atomic resolution, as well as simulation results. These results open up a new avenue for the application of XFH to local atomic and electronic structure imaging of metal-sites in biomolecules.


  • Organizational Affiliation

    Division of Biophysics, Department of Physiology, Jichi Medical University, Yakushiji, Shimotsuke, Tochigi, 329-0498, Japan. Electronic address: ayana.sato@jichi.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myoglobin151Physeter catodonMutation(s): 0 
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
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.93 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.403α = 90
b = 30.702β = 105.565
c = 63.804γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata collection
Cootmodel building
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan26105005

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description