5D8V

Ultra-high resolution structure of high-potential iron-sulfur protein

Summary for 5D8V

• Entry DOI: 10.2210/pdb5d8v/pdb
• Descriptor: High-potential iron-sulfur protein, IRON/SULFUR CLUSTER, SULFATE ION, ... (5 entities in total)
• Functional Keywords: iron-sulfur protein, metal binding protein
• Biological source: Thermochromatium tepidum
• Total number of polymer chains: 1
• Total formula weight: 9902.09

Authors

Hirano, Y.,Takeda, K.,Miki, K. (deposition date: 2015-08-18, release date: 2016-05-25, Last modification date: 2023-11-08)

Primary citation

Hirano, Y.,Takeda, K.,Miki, K.
Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 angstrom
Nature, 534:281-284, 2016

PubMed Abstract: The fine structures of proteins, such as the positions of hydrogen atoms, distributions of valence electrons and orientations of bound waters, are critical factors for determining the dynamic and chemical properties of proteins. Such information cannot be obtained by conventional protein X-ray analyses at 3.0-1.5 Å resolution, in which amino acids are fitted into atomically unresolved electron-density maps and refinement calculations are performed under strong restraints. Therefore, we usually supplement the information on hydrogen atoms and valence electrons in proteins with pre-existing common knowledge obtained by chemistry in small molecules. However, even now, computational calculation of such information with quantum chemistry also tends to be difficult, especially for polynuclear metalloproteins. Here we report a charge-density analysis of the high-potential iron-sulfur protein from the thermophilic purple bacterium Thermochromatium tepidum using X-ray data at an ultra-high resolution of 0.48 Å. Residual electron densities in the conventional refinement are assigned as valence electrons in the multipolar refinement. Iron 3d and sulfur 3p electron densities of the Fe4S4 cluster are visualized around the atoms. Such information provides the most detailed view of the valence electrons of the metal complex in the protein. The asymmetry of the iron-sulfur cluster and the protein environment suggests the structural basis of charge storing on electron transfer. Our charge-density analysis reveals many fine features around the metal complex for the first time, and will enable further theoretical and experimental studies of metalloproteins.

PubMed: 27279229
DOI: 10.1038/nature18001

Experimental method

X-RAY DIFFRACTION (0.48 Å)