2Q9E

Structure of spin-labeled T4 lysozyme mutant S44R1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural determinants of nitroxide motion in spin-labeled proteins: Solvent-exposed sites in helix B of T4 lysozyme.

Guo, Z.Cascio, D.Hideg, K.Hubbell, W.L.

(2008) Protein Sci. 17: 228-239

  • DOI: 10.1110/ps.073174008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Site-directed spin labeling provides a means for exploring structure and dynamics in proteins. To interpret the complex EPR spectra that often arise, it is necessary to characterize the rotamers of the spin-labeled side chain and the interactions the ...

    Site-directed spin labeling provides a means for exploring structure and dynamics in proteins. To interpret the complex EPR spectra that often arise, it is necessary to characterize the rotamers of the spin-labeled side chain and the interactions they make with the local environment in proteins of known structure. For this purpose, crystal structures have been determined for T4 lysozyme bearing a nitroxide side chain (R1) at the solvent-exposed helical sites 41 and 44 in the B helix. These sites are of particular interest in that the corresponding EPR spectra reveal two dynamic states of R1, one of which is relatively immobilized suggesting interactions of the nitroxide with the environment. The crystal structures together with the effect of mutagenesis of nearest neighbors on the motion of R1 suggest intrahelical interactions of 41R1 with the i + 4 residue and of 44R1 with the i + 1 residue. Such interactions appear to be specific to particular rotamers of the R1 side chain.


    Organizational Affiliation

    Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-7008, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme
A, B, C
164Enterobacteria phage T4Mutations: N55A, C97A, C54T
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HED
Query on HED

Download SDF File 
Download CCD File 
A, B
2-HYDROXYETHYL DISULFIDE
C4 H10 O2 S2
KYNFOMQIXZUKRK-UHFFFAOYSA-N
 Ligand Interaction
MTN
Query on MTN

Download SDF File 
Download CCD File 
A, B, C
S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
MTSL
C10 H18 N O3 S2
MXZPGYFBZHBAQM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.989α = 90.00
b = 67.140β = 90.00
c = 165.919γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-02-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Non-polymer description
  • Version 1.4: 2017-10-18
    Type: Advisory, Refinement description