30OH | pdb_000030oh

Pyrococcus abyssi Rubredoxin @ 0.43 Angstrom resolution, Transferable Aspherical Atom Model (TAAM) refinement

• PDB DOI: https://doi.org/10.2210/pdb30OH/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Pyrococcus abyssi GE5
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2026-05-05 Released: 2026-09-16 
• Deposition Author(s): 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.
• Funding Organization(s): Volkswagen Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.43 Å
• R-Value Free: 
  0.069 (Depositor), 0.079 (DCC) 
• R-Value Work: 
  0.065 (Depositor), 0.075 (DCC) 
• R-Value Observed: 
  0.065 (Depositor) 

Starting Model: experimental

Literature

Towards routine accurate electron-density studies of biological macromolecules.

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.

(2026) Acta Crystallogr D Struct Biol 82: 1044-1055

• PubMed: 42583823 
• DOI: https://doi.org/10.1107/S2059798326007448
• Primary Citation Related Structures: 
  30OH, 30OR


• 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.

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Organizational Affiliation: 
• Department of Structural Dynamics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.
Global Phasing Limited, 9 Journey Campus, Castle Park, Cambridge CB3 0AX, United Kingdom.
Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, ul. Zwirki I Wigury 101, 02-089 Warsaw, Poland.
DECTRIS Ltd, Täfernweg 1, 5405 Baden-Dättwil, Switzerland.
European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22607 Hamburg, Germany.
Research Group for Structural Biochemistry and Mechanisms, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 6.34 kDa 
• Atom Count: 785 
• Modeled Residue Count: 57 
• Deposited Residue Count: 57 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A	57	Pyrococcus abyssi GE5	Mutation(s): 0  Gene Names: rub, rd, PYRAB08920, PAB7224
UniProt
Find proteins for Q9V099 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V099  Go to UniProtKB:  Q9V099

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE (Subject of Investigation/LOI)	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA	C [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.43 Å
• R-Value Free:  0.069 (Depositor), 0.079 (DCC) 
• R-Value Work:  0.065 (Depositor), 0.075 (DCC) 
• R-Value Observed: 0.065 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.73	α = 90
b = 39.237	β = 90
c = 45.14	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
autoPROC	data processing
Aimless	data scaling
STARANISO	data scaling
BUSTER	phasing
BUSTER	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-16 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	0200374

Revision History  

• Version 1.0: 2026-09-16
  Type: Initial release