4DQ1 | pdb_00004dq1

Thymidylate synthase from Staphylococcus aureus.

• PDB DOI: https://doi.org/10.2210/pdb4DQ1/pdb

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


• Deposited: 2012-02-14 Released: 2012-03-21 
• Deposition Author(s): Osipiuk, J., Holowicki, J., Jedrzejczak, R., Rubin, E., Guinn, K., Ioerger, T., Baker, D., Sacchettini, J., Joachimiak, A., 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: 2.71 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Thymidylate synthase from Staphylococcus aureus.

Osipiuk, J., Holowicki, J., Jedrzejczak, R., Rubin, E., Guinn, K., Ioerger, T., Baker, D., Sacchettini, J., Joachimiak, A.

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: 74.9 kDa 
• Atom Count: 5,092 
• Modeled Residue Count: 612 
• Deposited Residue Count: 642 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	321	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: SAV1427, thyA EC: 2.1.1.45
UniProt
Find proteins for P67046 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore P67046  Go to UniProtKB:  P67046

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	C [auth A], D [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34DQ1

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.309	α = 90
b = 111.309	β = 90
c = 59.081	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Osipiuk, J., Holowicki, J., Jedrzejczak, R., Rubin, E., Guinn, K., Ioerger, T., Baker, D., Sacchettini, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description