2ALX | pdb_00002alx

Ribonucleotide Reductase R2 from Escherichia coli in space group P6(1)22

• PDB DOI: https://doi.org/10.2210/pdb2ALX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-08-08 Released: 2005-11-29 
• Deposition Author(s): Sommerhalter, M., Saleh, L., Bollinger Jr., J.M., Rosenzweig, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Structure of Escherichia coli ribonucleotide reductase R2 in space group P6122.

Sommerhalter, M., Saleh, L., Bollinger, J.M., Rosenzweig, A.C.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1649-1654

• PubMed: 16301799 
• DOI: https://doi.org/10.1107/S0907444905034062
• Primary Citation Related Structures: 
  2ALX


• PubMed Abstract: 
  

  A new crystal form of wild-type ribonucleotide reductase R2 from Escherichia coli was obtained. Crystals grow in space group P6(1)22 with one R2 monomer in the asymmetric unit. A twofold crystallographic symmetry axis generates the physiological dimeric form of R2. Co-crystallization with CoCl(2) or MnCl(2) results in full occupancy of the dinuclear metal site. The structure of the Mn(II)-loaded form was determined to 2.6 Angstroms resolution by molecular replacement. The crystallization conditions, backbone conformation, crystal-packing interactions and metal centers are compared with those of previously determined crystal forms.

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Organizational Affiliation: 
• Department of Biochemistry, Northwestern University, Evanston, IL 60208, USA.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 40.55 kDa 
• Atom Count: 2,788 
• Modeled Residue Count: 339 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase 1	A	340	Escherichia coli	Mutation(s): 0  Gene Names: nrdB, ftsB 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	D [auth A], E [auth A], F [auth A], G [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.94	α = 90
b = 92.94	β = 90
c = 200.93	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-29 
Deposition Author(s): Sommerhalter, M., Saleh, L., Bollinger Jr., J.M., Rosenzweig, A.C.

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description