30OR

Pyrococcus abyssi Rubredoxin @ 0.43 Angstrom resolution, Independent Atom Model (IAM) refinement

Summary for 30OR

• Entry DOI: 10.2210/pdb30or/pdb
• Descriptor: Rubredoxin, FE (III) ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: rubredoxin, electron tranport, electron transport
• Biological source: Pyrococcus abyssi GE5
• Total number of polymer chains: 1
• Total formula weight: 6337.68

Authors

Paknia, E.,Flensburg, C.,Chodkiewicz, M.L.,Fogh, R.,Keller, P.,Vonrhein, C.,Schulze-Briese, C.,Dominiak, P.M.,Bourenkov, G.,Bricogne, G.,Chari, A. (deposition date: 2026-05-06, release date: 2026-09-16)

Primary citation

Paknia, E.,Flensburg, C.,Chodkiewicz, M.L.,Fogh, R.H.,Keller, P.,Vonrhein, C.,Schulze-Briese, C.,Dominiak, P.M.,Bourenkov, G.,Bricogne, G.,Chari, A.
Towards routine accurate electron-density studies of biological macromolecules.
Acta Crystallogr D Struct Biol, 82:1044-1055, 2026

PubMed Abstract: We report here the structure of Pyrococcus abyssi rubredoxin determined at a resolution of 0.43 Å. This, to the best of our knowledge, represents the highest resolution protein structure yet determined. Experimentally, the determination of this structure has been made possible by a series of technical innovations and streamlined procedures that are described herein. The structure model refined with spherical scattering factors, the so-called independent atom model (IAM), reveals many positive difference densities that can be attributed to electrons at the midpoint of chemical bonds. To validate the interpretation that these do indeed represent bonding electrons, we have connected the DiSCaMB transferable aspherical atom model (TAAM) library to BUSTER. TAAM refinements resolve all positive density features in midpoints of chemical bonds. Extrapolating the findings and methodology reported here, we anticipate that it should now be possible to routinely acquire accurate X-ray diffraction data for quantum crystallography of biological macromolecules. This is particularly relevant to the study of enzyme mechanisms, which are well documented to entail quantum-mechanical phenomena.

PubMed: 42583823
DOI: 10.1107/S2059798326007448

Experimental method

X-RAY DIFFRACTION (0.434 Å)