2PYA

Ultra-high resolution structure of P. abyssi rubredoxin W4L/R5S/A44S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.86 Å
  • R-Value Free: 0.105 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin: II. Introduction of an O-H...Sgamma-Fe hydrogen bond increased the reduction potential by 65 mV.

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

(2007) J.Biol.Inorg.Chem. 12: 1163-1171

  • DOI: 10.1007/s00775-007-0289-8

  • PubMed Abstract: 
  • The effect of D-H...S(gamma)-Fe hydrogen bonding on the reduction potential of rubredoxin was investigated by the introduction of an O-H...S(gamma)-Fe hydrogen bond on the surface of Pyrococcus abyssi rubredoxin. The formation of a weak hydrogen bond ...

    The effect of D-H...S(gamma)-Fe hydrogen bonding on the reduction potential of rubredoxin was investigated by the introduction of an O-H...S(gamma)-Fe hydrogen bond on the surface of Pyrococcus abyssi rubredoxin. The formation of a weak hydrogen bond between Ser44-O(gamma) and Cys42-S(gamma) in mutant W4L/R5S/A44S increased the reduction potential by 56 mV. When side effects of the mutation were taken into account, the contribution of the additional cluster hydrogen bond to the reduction potential was estimated to be +65 mV. The structural analysis was based on ultrahigh-resolution structures of oxidized P. abyssi rubredoxin W4L/R5S and W4L/R5S/A44S refined to 0.69 and 0.86 A, respectively.


    Organizational Affiliation

    Center of Biosciences, Karolinska Institutet, Hälsovägen 7-9, 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): 3 
Gene Names: rub (rd)
Find proteins for Q9V099 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V099
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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: 0.86 Å
  • R-Value Free: 0.105 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 25.385α = 90.00
b = 39.812β = 90.00
c = 45.117γ = 90.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SCALEPACKdata scaling
SHELXDphasing
SHELXL-97refinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance