1R0J

nickel-substituted rubredoxin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Metal-substituted derivatives of the rubredoxin from Clostridium pasteurianum.

Maher, M.Cross, M.Wilce, M.C.Guss, J.M.Wedd, A.G.

(2004) Acta Crystallogr.,Sect.D 60: 298-303

  • DOI: 10.1107/S090744490302794X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Five different metal-substituted forms of Clostridium pasteurianum rubredoxin have been prepared and crystallized. The single Fe atom present in the Fe(S-Cys)(4) site of the native form of the protein was exchanged in turn for Co, Ni, Ga, Cd and Hg. ...

    Five different metal-substituted forms of Clostridium pasteurianum rubredoxin have been prepared and crystallized. The single Fe atom present in the Fe(S-Cys)(4) site of the native form of the protein was exchanged in turn for Co, Ni, Ga, Cd and Hg. All five forms of rubredoxin crystallized in space group R3 and were isomorphous with the native protein. The Co-, Ni- and Ga-substituted proteins exhibited metal sites with geometries similar to that of the Fe form (effective D(2d) local symmetry), as did the Cd and Hg proteins, but with a significant expansion of the metal-sulfur bond lengths. A knowledge of these structures contributes to a molecular understanding of the function of this simple iron-sulfur electron-transport protein.


    Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, New South Wales 2006, Australia. m.maher@mmb.usyd.edu.au




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rubredoxin
A
54Clostridium pasteurianumMutation(s): 0 
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download SDF File 
Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.219 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 64.331α = 90.00
b = 64.331β = 90.00
c = 32.120γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance