4DWJ

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

• PDB DOI: https://doi.org/10.2210/pdb4DWJ/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-24 Released: 2012-03-07 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.268 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with Thymidine Monophosphate

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Jedrzejczak, R., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 211.84 kDa 
• Atom Count: 12,937 
• Modelled Residue Count: 1,589 
• Deposited Residue Count: 1,832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B, C, D, E, F, G, H	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TMP	I [auth A], J [auth B], K [auth C], L [auth D], M [auth F], N [auth G], O [auth H]	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 0.268 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/M34DWJ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.662	α = 81.48
b = 73.409	β = 90.1
c = 96.868	γ = 90.12

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
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: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Structure summary
• Version 1.2: 2012-10-10
  Changes: Structure summary
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description