Ultra-high resolution structure of Pyrococcus abyssi rubredoxin W4L/R5S

Experimental Data Snapshot

  • Resolution: 0.69 Å
  • R-Value Free: 0.108 
  • R-Value Work: 0.100 
  • R-Value Observed: 0.100 

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Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.

Bonisch, H.Schmidt, C.L.Bianco, P.Ladenstein, R.

(2005) Acta Crystallogr D Biol Crystallogr 61: 990-1004

  • DOI: https://doi.org/10.1107/S090744490501293X
  • Primary Citation of Related Structures:  
    1YK4, 1YK5

  • PubMed Abstract: 

    The crystal structure of Pyrococcus abyssi rubredoxin mutant W4L/R5S was solved by direct methods. The model of the air-oxidized protein was refined by partially restrained full-matrix least-squares refinement against intensity data to 0.69 A resolution. This first ultrahigh-resolution structure of a rubredoxin provides very detailed and precise information about the Fe(SCys)(4) centre and its environment, the peptide-backbone stereochemistry, H atoms and hydrogen bonds, static and dynamic disorder, the solvent structure and the electron-density distribution. P. abyssi rubredoxin W4L/R5S is the first of a series of mutants studied by atomic and ultrahigh-resolution X-ray crystallography which are expected to contribute to the understanding of structure-function relationships in iron-sulfur proteins.

  • Organizational Affiliation

    Karolinska Institutet, Department of Biosciences at NOVUM, Center for Structural Biochemistry, Hälsovägen 7-9, S-14157 Huddinge, Sweden. heiko.bonisch@csb.ki.se

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rubredoxin52Pyrococcus abyssiMutation(s): 2 
Gene Names: rub
Find proteins for Q9V099 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V099 
Go to UniProtKB:  Q9V099
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V099
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Experimental Data & Validation

Experimental Data

  • Resolution: 0.69 Å
  • R-Value Free: 0.108 
  • R-Value Work: 0.100 
  • R-Value Observed: 0.100 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.14α = 90
b = 39.5β = 90
c = 45.07γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Data collection, Database references, Derived calculations