2P1I

Plasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671)

• PDB DOI: https://doi.org/10.2210/pdb2P1I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium yoelii yoelii 17XNL
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-05 Released: 2007-03-27 
• Deposition Author(s): Wernimont, A.K., Dong, A., Choe, J., Gao, M., Walker, J., Lew, J., Alam, Z., Zhao, Y., Nordlund, P., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Artz, J.D., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.368 (Depositor), 0.350 (DCC) 
• R-Value Work: 
  0.304 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.307 (Depositor) 

Starting Model: experimental

Literature

Plasmodium yoelii Ribonucleotide Reductase Subunit R2 (PY03671)

Wernimont, A.K., Dong, A., Choe, J., Gao, M., Walker, J., Lew, J., Alam, Z., Zhao, Y., Nordlund, P., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Artz, J.D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 324.38 kDa 
• Atom Count: 16,904 
• Modelled Residue Count: 2,050 
• Deposited Residue Count: 2,792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleotide reductase, small chain	A, B, C, D, E, F, G, H	349	Plasmodium yoelii yoelii 17XNL	Mutation(s): 0  Gene Names: PY03671
UniProt
Find proteins for Q7RIF3 (Plasmodium yoelii yoelii) Explore Q7RIF3  Go to UniProtKB:  Q7RIF3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.368 (Depositor), 0.350 (DCC) 
• R-Value Work:  0.304 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.307 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.04	α = 90
b = 153.46	β = 132
c = 143.36	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Wernimont, A.K., Dong, A., Choe, J., Gao, M., Walker, J., Lew, J., Alam, Z., Zhao, Y., Nordlund, P., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Sundstrom, M., Bochkarev, A., Hui, R., Artz, J.D., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary