2X5F

Crystal structure of the methicillin-resistant Staphylococcus aureus Sar2028, an aspartate_tyrosine_phenylalanine pyridoxal-5'-phosphate dependent aminotransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.

Oke, M.Carter, L.G.Johnson, K.A.Liu, H.Mcmahon, S.A.Yan, X.Kerou, M.Weikart, N.D.Kadi, N.Sheikh, M.A.Schmelz, S.Dorward, M.Zawadzki, M.Cozens, C.Falconer, H.Powers, H.Overton, I.M.Van Niekerk, C.A.J.Peng, X.Patel, P.Garrett, R.A.Prangishvili, D.Botting, C.H.Coote, P.J.Dryden, D.T.F.Barton, G.J.Schwarz-Linek, U.Challis, G.L.Taylor, G.L.White, M.F.Naismith, J.H.

(2010) J Struct Funct Genomics 11: 167

  • DOI: 10.1007/s10969-010-9090-y
  • Primary Citation of Related Structures:  
    2WJ9, 2X0O, 2X3E, 2X3F, 2X3G, 2X3L, 2X3D, 2X4G, 2X4H, 2X4I

  • PubMed Abstract: 
  • The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed ...

    The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.


    Related Citations: 
    • Expression, Purification, Crystallization, Data Collection and Preliminary Biochemical Characterization of Methicillin-Resistant Staphylococcus Aureus Sar2028, an Aspartate/Tyrosine/Phenylalanine Pyridoxal-5'-Phosphate-Dependent Aminotransferase.
      Seetharamappa, J., Oke, M., Liu, H., Mcmahon, S.A., Johnson, K.A., Carter, L., Dorward, M., Zawadzki, M., Overton, I.M., Van Niekirk, C.A.J., Graham, S., Botting, C.H., Taylor, G.L., White, M.F., Barton, G.J., Coote, P.J., Naismith, J.H.
      (2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 452

    Organizational Affiliation

    Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASEA, B430Staphylococcus aureus subsp. aureus MRSA252Mutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.78α = 90
b = 89.99β = 90
c = 104.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing
SOLVEphasing
RESOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance