2DSX

Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.68 Å
  • R-Value Free: 0.111 
  • R-Value Work: 0.099 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68A resolution

Chen, C.J.Lin, Y.H.Huang, Y.C.Liu, M.Y.

(2006) Biochem.Biophys.Res.Commun. 349: 79-90

  • DOI: 10.1016/j.bbrc.2006.07.205

  • PubMed Abstract: 
  • Rubredoxin (D.g. Rd) is a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria Desulfovibrio gigas. The protein is generally purified from anaerobic bacteria in which it is thought to be ...

    Rubredoxin (D.g. Rd) is a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria Desulfovibrio gigas. The protein is generally purified from anaerobic bacteria in which it is thought to be involved in electron transfer or exchange processes. Rd transfers an electron to oxygen to form water as part of a unique electron transfer chain, composed by NADH:rubredoxin oxidoreductase (NRO), rubredoxin and rubredoxin:oxygen oxidoreductase (ROO) in D.g. The crystal structure of D.g. Rd has been determined by means of both a Fe single-wavelength anomalous dispersion (SAD) signal and the direct method, and refined to an ultra-high 0.68 A resolution, using X-ray from a synchrotron. Rd contains one iron atom bound in a tetrahedral coordination by the sulfur atoms of four cysteinyl residues. Hydrophobic and pi-pi interactions maintain the internal Rd folding. Multiple conformations of the iron-sulfur cluster and amino acid residues are observed and indicate its unique mechanism of electron transfer. Several hydrogen bonds, including N-H...SG of the iron-sulfur, are revealed clearly in maps of electron density. Abundant waters bound to C-O peptides of residues Val8, Cys9, Gly10, Ala38, and Gly43, which may be involved in electron transfer. This ultrahigh-resolution structure allows us to study in great detail the relationship between structure and function of rubredoxin, such as salt bridges, hydrogen bonds, water structures, cysteine ligands, iron-sulfur cluster, and distributions of electron density among activity sites. For the first time, this information will provide a clear role for this protein in a strict anaerobic bacterium.


    Organizational Affiliation

    Life Science Group, Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan. cjchen@nsrrc.org.tw




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rubredoxin
A
52Desulfovibrio gigasN/A
Find proteins for P00270 (Desulfovibrio gigas)
Go to UniProtKB:  P00270
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: 0.68 Å
  • R-Value Free: 0.111 
  • R-Value Work: 0.099 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 19.474α = 90.00
b = 41.324β = 108.20
c = 24.129γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
SHELXL-97refinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance