1OQU

A protein coordinated tri-nuclear Fe complex formed during soaking of crystals of the ribonucleotide reductase R2F protein from Corynebacterium Ammoniagenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A protein carboxylate coordinated oxo-centered tri-nuclear iron complex with possible implications for ferritin mineralization

Hogbom, M.Nordlund, P.

(2004) Febs Lett. 567: 179-182

  • DOI: 10.1016/j.febslet.2004.04.068

  • PubMed Abstract: 
  • The crystal structure of an oxo-centered tri-nuclear iron complex formed on a protein surface is presented. The cluster forms when crystals of the class Ib ribonucleotide reductase R2 protein from Corynebacterium ammoniagenes are subjected to iron so ...

    The crystal structure of an oxo-centered tri-nuclear iron complex formed on a protein surface is presented. The cluster forms when crystals of the class Ib ribonucleotide reductase R2 protein from Corynebacterium ammoniagenes are subjected to iron soaking. The tri-iron-oxo complex is coordinated by protein-derived carboxylate ligands arranged in a motif similar to the one found on the inner surface of ferritins and may mimic an early stage in the mineralization of iron in ferritins. In addition, the structure adds to the very limited data on protein-mineral interfaces.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Stockholm University Roslagstullsbacken 15, Albanova University Center, Stockholm SE-106 91, Sweden. hogbom@dbb.su.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ribonucleotide reductase subunit R2F
A, B, C, D
329Corynebacterium ammoniagenesGene Names: nrdF
EC: 1.17.4.1
Find proteins for O69274 (Corynebacterium ammoniagenes)
Go to UniProtKB:  O69274
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A, C, D
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.319α = 90.00
b = 91.237β = 91.46
c = 136.956γ = 90.00
Software Package:
Software NamePurpose
ProDCdata collection
CNSphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description