7VDN image
Deposition Date 2021-09-07
Release Date 2022-09-14
Last Version Date 2023-11-29
Entry Detail
PDB ID:
7VDN
Title:
High resolution crystal structure of Sperm Whale Myoglobin in the carbonmonoxy form
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
0.93 Å
R-Value Free:
0.21
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Myoglobin
Gene (Uniprot):MB
Chain IDs:A
Chain Length:151
Number of Molecules:1
Biological Source:Physeter catodon
Primary Citation
X-ray fluorescence holography of biological metal sites: Application to myoglobin.
Biochem.Biophys.Res.Commun. 635 277 282 (2022)
PMID: 36308907 DOI: 10.1016/j.bbrc.2022.10.003

Abstact

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.

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