2X3L

Crystal Structure of the Orn_Lys_Arg decarboxylase family protein SAR0482 from Methicillin-resistant Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1007/s10969-010-9090-y
  • Primary Citation of Related Structures:  
    2IVY, 2JG5, 2JG6, 2VW8, 2VXZ, 2WJ9, 2X0O, 2X3D, 2X3E, 2X3F, 2X3G, 2X3L, 2X3M, 2X3N, 2X3O, 2X48, 2X4G, 2X4H, 2X4I, 2X4J, 2X4K, 2X4L, 2X5C, 2X5D, 2X5F, 2X5G, 2X5H, 2X5P, 2X5Q, 2X5R, 2X5T, 2X7B, 2X7I, 2XU2

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN
A, B
446Staphylococcus aureusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
SM
Query on SM

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
SAMARIUM (III) ION
Sm
DOSGOCSVHPUUIA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
H [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.677α = 90
b = 137.283β = 109.64
c = 62.258γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2015-11-11
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance