4EAQ | pdb_00004eaq

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with 3'-Azido-3'-Deoxythymidine-5'-Monophosphate

• PDB DOI: https://doi.org/10.2210/pdb4EAQ/pdb

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


• Deposited: 2012-03-22 Released: 2012-04-11 
• 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: 1.85 Å
• R-Value Free: 
  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Thymidylate Kinase from Staphylococcus aureus in complex with 3'-Azido-3'-Deoxythymidine-5'-Monophosphate

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

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: 53.09 kDa 
• Atom Count: 3,400 
• Modeled Residue Count: 398 
• 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATM	C [auth A], D [auth B]	3'-AZIDO-3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE C10 H14 N5 O7 P OIFWQOKDSPDILA-XLPZGREQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.229 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34EAQ

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.207	α = 90
b = 62.704	β = 97.84
c = 73.806	γ = 90

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