1YK4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.69 Å
  • R-Value Free: 0.108 
  • R-Value Work: 0.100 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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.,Sect.D 61: 990-1004

  • DOI: 10.1107/S090744490501293X
  • Primary Citation of Related Structures:  

  • 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 resolut ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rubredoxin
A
52Pyrococcus abyssi (strain GE5 / Orsay)Mutation(s): 2 
Gene Names: rub (rd)
Find proteins for Q9V099 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V099
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.69 Å
  • R-Value Free: 0.108 
  • R-Value Work: 0.100 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.140α = 90.00
b = 39.500β = 90.00
c = 45.070γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
SHELXL-97refinement
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance