3S87 | pdb_00003s87

Structure of Yeast Ribonucleotide Reductase 1 with dGTP and ADP

• PDB DOI: https://doi.org/10.2210/pdb3S87/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-27 Released: 2012-04-11 
• Deposition Author(s): Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.261 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Structural and biochemical basis of lethal mutant R293A of yeast ribonucleotide reductase

Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C.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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 100.63 kDa 
• Atom Count: 5,544 
• Modeled Residue Count: 664 
• Deposited Residue Count: 888 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase large chain 1	A	888	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: CRT7, RIR1, RNR1, Saccharomyces, SDS12, YER070W EC: 1.17.4.1
UniProt
Find proteins for P21524 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21524  Go to UniProtKB:  P21524

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT	C [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N
ADP	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.261 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.618	α = 90
b = 117.191	β = 90
c = 65.524	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Ahmad, M.F., Kaushal, P.S., Wan, Q., Wijeratna, S.R., Huang, M., Dealwis, C.D.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description