4F4I

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in apo-form

• PDB DOI: https://doi.org/10.2210/pdb4F4I/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-10 Released: 2012-05-23 
• Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.242 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in apo-form

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
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 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 52.4 kDa 
• Atom Count: 3,168 
• Modelled Residue Count: 390 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	229	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: tmk, SAV0482 EC: 2.7.4.9
UniProt
Find proteins for P65248 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P65248  Go to UniProtKB:  P65248

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.242 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34F4I

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.099	α = 90
b = 91.022	β = 104.47
c = 47.498	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-23 
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Babnigg, G., Rubin, E., Sacchettini, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History  

• Version 1.0: 2012-05-23
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2017-11-29
  Changes: Database references
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description