2XJ3

High resolution structure of the T55C mutant of CylR2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.184 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Integrated Analysis of the Conformation of a Protein-Linked Spin Label by Crystallography, Epr and NMR Spectroscopy.

Gruene, T.Cho, M.K.Karyagina, I.Kim, H.Y.Grosse, C.Giller, K.Zweckstetter, M.Becker, S.

(2011) J Biomol NMR 49: 111

  • DOI: 10.1007/s10858-011-9471-y
  • Primary Citation of Related Structures:  
    2XI8, 2XIU, 2XJ3

  • PubMed Abstract: 
  • Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as protein-protein and protein-DNA complexes ...

    Long-range structural information derived from paramagnetic relaxation enhancement observed in the presence of a paramagnetic nitroxide radical is highly useful for structural characterization of globular, modular and intrinsically disordered proteins, as well as protein-protein and protein-DNA complexes. Here we characterized the conformation of a spin-label attached to the homodimeric protein CylR2 using a combination of X-ray crystallography, electron paramagnetic resonance (EPR) and NMR spectroscopy. Close agreement was found between the conformation of the spin label observed in the crystal structure with interspin distances measured by EPR and signal broadening in NMR spectra, suggesting that the conformation seen in the crystal structure is also preferred in solution. In contrast, conformations of the spin label observed in crystal structures of T4 lysozyme are not in agreement with the paramagnetic relaxation enhancement observed for spin-labeled CylR2 in solution. Our data demonstrate that accurate positioning of the paramagnetic center is essential for high-resolution structure determination.


    Organizational Affiliation

    Department of Structural Chemistry, University of Göttingen, Tammannstraße 4, 37077, Göttingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYLR2 SYNONYM CYTOLYSIN REPRESSOR 2A, B66Enterococcus faecalisMutation(s): 1 
Gene Names: cylR2BZG32_02305CUN08_03990CYQ48_15935ELS84_2076GTI65_14965
UniProt
Find proteins for Q8VL32 (Enterococcus faecalis)
Explore Q8VL32 
Go to UniProtKB:  Q8VL32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VL32
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.23 Å
  • R-Value Free: 0.184 
  • R-Value Observed: 0.150 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.45α = 90
b = 63.45β = 90
c = 41.2γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-09
    Type: Initial release
  • Version 1.1: 2011-05-19
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description