2R2F

RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM SALMONELLA TYPHIMURIUM (OXIDIZED)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms.

Eriksson, M.Jordan, A.Eklund, H.

(1998) Biochemistry 37: 13359-13369

  • DOI: 10.1021/bi981380s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The first class Ib ribonucleotide reductase R2 structure, from Salmonella typhimurium, has been determined at 2.0 A resolution. The overall structure is similar to the Escherichia coli class Ia enzyme despite only 23% sequence identity. The most spec ...

    The first class Ib ribonucleotide reductase R2 structure, from Salmonella typhimurium, has been determined at 2.0 A resolution. The overall structure is similar to the Escherichia coli class Ia enzyme despite only 23% sequence identity. The most spectacular difference is the absence of the pleated sheet and adjacent parts present in the E. coli R2 structure; the heart-shaped structure loses its tip. From sequence comparisons, it appears that this feature is shared with all other class Ib enzymes and, in this respect, is more like the mammalian class Ia enzymes. Both the oxidized and reduced iron forms have been investigated. In the ferric iron center, both iron ions are octahedrally coordinated and bridged by one carboxylate and one oxide ion. The ferrous form has lost the bridging oxide ion but is bridged by two carboxylates. Accompanying the change in redox state, helix E changes its conformation from one covering the metal center in the oxidized form to a more open reduced form. A narrow channel is opened which may permit easier access of oxygen to the ferrous iron site and to efficiently generate the tyrosyl radical.


    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN)
A, B
319Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: nrdF
EC: 1.17.4.1
Find proteins for P17424 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P17424
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEO
Query on FEO

Download SDF File 
Download CCD File 
A, B
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.490α = 90.00
b = 71.740β = 95.01
c = 96.070γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance