3H5Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrimidine-nucleoside phosphorylase
A
436Staphylococcus aureus (strain COL)Gene Names: pdp (pyn)
EC: 2.4.2.2
Find proteins for Q5HE64 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  Q5HE64
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
THM
Query on THM

Download SDF File 
Download CCD File 
A
THYMIDINE
DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE
C10 H14 N2 O5
IQFYYKKMVGJFEH-XLPZGREQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 51.591α = 90.00
b = 40.885β = 97.19
c = 105.578γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DMphasing
SHELXDphasing
RESOLVEphasing
HKL-3000data reduction
HKL-3000phasing
RESOLVEmodel building
HKL-3000data scaling
MLPHAREphasing
HKL-3000data collection
DMmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance