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: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1016/j.febslet.2004.04.068
  • Primary Citation of Related Structures:  
    1OQU

  • 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 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ribonucleotide reductase subunit R2F
A, B, C, D
329Corynebacterium ammoniagenesMutation(s): 0 
UniProt
Find proteins for O69274 (Corynebacterium ammoniagenes)
Explore O69274 
Go to UniProtKB:  O69274
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO69274
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT
Download Ideal Coordinates CCD File 
U [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE
Query on FE
Download Ideal Coordinates CCD File 
AA [auth D]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
OXY
Query on OXY
Download Ideal Coordinates CCD File 
BA [auth D],
J [auth A],
V [auth C]		OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.319α = 90
b = 91.237β = 91.459
c = 136.956γ = 90
Software Package:
Software NamePurpose
ProDCdata collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations