3H5Q

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb3H5Q/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus subsp. aureus COL
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-04-22 Released: 2009-05-26 
• Deposition Author(s): Shumilin, I.A., Zimmerman, M., Cymborowski, M., Skarina, T., Onopriyenko, O., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal structure of a putative pyrimidine-nucleoside phosphorylase from Staphylococcus aureus

Shumilin, I.A., Zimmerman, M., Cymborowski, M., Skarina, T., Onopriyenko, O., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 47.85 kDa 
• Atom Count: 3,729 
• Modelled Residue Count: 436 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrimidine-nucleoside phosphorylase	A	436	Staphylococcus aureus subsp. aureus COL	Mutation(s): 1  Gene Names: pdp, pyn, SACOL2128 EC: 2.4.2.2
UniProt
Find proteins for Q5HE64 (Staphylococcus aureus (strain COL)) Explore Q5HE64  Go to UniProtKB:  Q5HE64

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THM	B [auth A]	THYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33H5Q

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.591	α = 90
b = 40.885	β = 97.19
c = 105.578	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Shumilin, I.A., Zimmerman, M., Cymborowski, M., Skarina, T., Onopriyenko, O., Anderson, W.F., Savchenko, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2021-10-13
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary