Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89656.72 
• Atom Count: 5583 
• Residue Count: 750 
• Unique protein chains: 1

1R65

Crystal structure of ferrous soaked Ribonucleotide Reductase R2 subunit (wildtype) at pH 5 from E. coli

• DOI: 10.2210/pdb1R65/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli


• Deposited: 2003-10-14 Released: 2004-01-13 
• Deposition Author(s): Voegtli, W.C., Sommerhalter, M., Saleh, L., Baldwin, J., Bollinger Jr., J.M., Rosenzweig, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.207 

Literature

Variable coordination geometries at the diiron(II) active site of ribonucleotide reductase R2.

Voegtli, W.C., Sommerhalter, M., Saleh, L., Baldwin, J., Bollinger Jr., J.M., Rosenzweig, A.C.

(2003) J.Am.Chem.Soc. 125: 15822-15830

• PubMed: 14677973 
• DOI: 10.1021/ja0370387
• Primary Citation of Related Structures:  
  1PM2, 1PJ1, 1PJ0, 1PIZ, 1PIY


• PubMed Abstract: 
  

The R2 subunit of Escherichia coli ribonucleotide reductase contains a dinuclear iron center that generates a catalytically essential stable tyrosyl radical by one electron oxidation of a nearby tyrosine residue. After acquisition of Fe(II) ions by the apo protein, the resulting diiron(II) center reacts with O(2) to initiate formation of the radical. Knowledge of the structure of the reactant diiron(II) form of R2 is a prerequisite for a detailed understanding of the O(2) activation mechanism. Whereas kinetic and spectroscopic studies of the reaction have generally been conducted at pH 7.6 with reactant produced by the addition of Fe(II) ions to the apo protein, the available crystal structures of diferrous R2 have been obtained by chemical or photoreduction of the oxidized diiron(III) protein at pH 5-6. To address this discrepancy, we have generated the diiron(II) states of wildtype R2 (R2-wt), R2-D84E, and R2-D84E/W48F by infusion of Fe(II) ions into crystals of the apo proteins at neutral pH. The structures of diferrous R2-wt and R2-D48E determined from these crystals reveal diiron(II) centers with active site geometries that differ significantly from those observed in either chemically or photoreduced crystals. Structures of R2-wt and R2-D48E/W48F determined at both neutral and low pH are very similar, suggesting that the differences are not due solely to pH effects. The structures of these "ferrous soaked" forms are more consistent with circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopic data and provide alternate starting points for consideration of possible O(2) activation mechanisms.

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Organizational Affiliation: 

Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ribonucleoside-diphosphate reductase 1 beta chain	A, B	375	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: nrdB (ftsB) EC: 1.17.4.1
Find proteins for P69924 (Escherichia coli (strain K12)) Go to UniProtKB:  P69924

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FE2	A, B	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
HG	A, B	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.236 
• R-Value Work: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 74.170	α = 90.00
b = 84.220	β = 90.00
c = 114.220	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-10-14 
• Released Date: 2004-01-13 
• Deposition Author(s): Voegtli, W.C., Sommerhalter, M., Saleh, L., Baldwin, J., Bollinger Jr., J.M., Rosenzweig, A.C.

Revision History 

• Version 1.0: 2004-01-13
  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: 2018-02-14
  Type: Experimental preparation