3E2I

Crystal structure of Thymidine Kinase from S. aureus

• PDB DOI: https://doi.org/10.2210/pdb3E2I/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-05 Released: 2009-08-11 
• Deposition Author(s): Lam, R., Johns, K., Battaile, K.P., Romanov, V., Lam, K., Pai, E.F., Chirgadze, N.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of Thymidine Kinase from S. aureus

Lam, R., Johns, K., Battaile, K.P., Romanov, V., Lam, K., Pai, E.F., Chirgadze, N.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 24.9 kDa 
• Atom Count: 1,414 
• Modelled Residue Count: 175 
• Deposited Residue Count: 219 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine kinase	A	219	Staphylococcus aureus	Mutation(s): 0  Gene Names: tdk EC: 2.7.1.21
UniProt
Find proteins for Q0H0G9 (Staphylococcus aureus) Explore Q0H0G9  Go to UniProtKB:  Q0H0G9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.237 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.621	α = 90
b = 71.621	β = 90
c = 96.144	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Lam, R., Johns, K., Battaile, K.P., Romanov, V., Lam, K., Pai, E.F., Chirgadze, N.Y.

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary