1PIM

DITHIONITE REDUCED E. COLI RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT, D84E MUTANT

• PDB DOI: https://doi.org/10.2210/pdb1PIM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-05-30 Released: 2003-06-17 
• Deposition Author(s): Voegtli, W.C., Khidekel, N., Baldwin, J., Ley, B.A., Bollinger Jr., J.M., Rosenzweig, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Crystal Structure of the Ribonucleotide Reductase R2 Mutant that Accumulates a u-1,2-Peroxodiiron(III) Intermediate during Oxygen Activation

Voegtli, W.C., Khidekel, N., Baldwin, J., Ley, B.A., Bollinger Jr., J.M., Rosenzweig, A.C.

(2000) J Am Chem Soc 122: 3255-3261

• DOI: https://doi.org/10.1021/ja991839l

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 88.48 kDa 
• Atom Count: 5,781 
• Modelled Residue Count: 680 
• Deposited Residue Count: 750 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase 1 beta chain	A, B	375	Escherichia coli	Mutation(s): 1  Gene Names: RIR2 EC: 1.17.4.1
UniProt
Find proteins for P69924 (Escherichia coli (strain K12)) Explore P69924  Go to UniProtKB:  P69924

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
FE	C [auth A], D [auth A], H [auth B], I [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.1	α = 90
b = 84.6	β = 90
c = 114.8	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-17 
Deposition Author(s): Voegtli, W.C., Khidekel, N., Baldwin, J., Ley, B.A., Bollinger Jr., J.M., Rosenzweig, A.C.

Revision History  

• Version 1.0: 2003-06-17
  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: 2021-10-27
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-14
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Refinement description