4MQB | pdb_00004mqb

Crystal structure of thymidylate kinase from Staphylococcus aureus in complex with 2-(N-morpholino)ethanesulfonic acid

• PDB DOI: https://doi.org/10.2210/pdb4MQB/pdb

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


• Deposited: 2013-09-16 Released: 2013-10-23 
• 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.198 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thymidylate kinase from Staphylococcus aureus in complex with 2-(N-morpholino)ethanesulfonic acid

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: 48.41 kDa 
• Atom Count: 3,719 
• Modeled Residue Count: 406 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	208	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4	D [auth A], E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.198 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.134	α = 90
b = 90.457	β = 101.64
c = 49.524	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: 2013-10-23 
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: 2013-10-23
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-09
  Changes: Structure summary