Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.0 of the entry. See complete history


A Highly Ordered Nitroxide Side Chain for Distance Mapping and Monitoring Slow Structural Fluctuations in Proteins.

Chen, M.Kalai, T.Cascio, D.Bridges, M.D.Whitelegge, J.P.Elgeti, M.Hubbell, W.L.

(2024) Appl Magn Reson 55: 251-277

  • DOI: https://doi.org/10.1007/s00723-023-01618-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Site-directed spin labeling electron paramagnetic resonance (SDSL-EPR) is an established tool for exploring protein structure and dynamics. Although nitroxide side chains attached to a single cysteine via a disulfide linkage are commonly employed in SDSL-EPR, their internal flexibility complicates applications to monitor slow internal motions in proteins and to structure determination by distance mapping. Moreover, the labile disulfide linkage prohibits the use of reducing agents often needed for protein stability. To enable the application of SDSL-EPR to the measurement of slow internal dynamics, new spin labels with hindered internal motion are desired. Here, we introduce a highly ordered nitroxide side chain, designated R9, attached at a single cysteine residue via a non-reducible thioether linkage. The reaction to introduce R9 is highly selective for solvent-exposed cysteine residues. Structures of R9 at two helical sites in T4 Lysozyme were determined by X-ray crystallography and the mobility in helical sequences was characterized by EPR spectral lineshape analysis, Saturation Transfer EPR, and Saturation Recovery EPR. In addition, interspin distance measurements between pairs of R9 residues are reported. Collectively, all data indicate that R9 will be useful for monitoring slow internal structural fluctuations, and applications to distance mapping via dipolar spectroscopy and relaxation enhancement methods are anticipated. The online version contains supplementary material available at 10.1007/s00723-023-01618-8.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endolysin162Escherichia phage T4Mutation(s): 4 
Find proteins for A0A7S9SVX7 (Escherichia phage T4)
Explore A0A7S9SVX7 
Go to UniProtKB:  A0A7S9SVX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7S9SVX7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GFX (Subject of Investigation/LOI)
Query on GFX

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
methyl 1-hydroxy-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrole-3-carboxylate, radical
C10 H17 N O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.39α = 90
b = 60.39β = 90
c = 95.43γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateUnited StatesJules Stein Professorship endowment
Hungarian National Research, Development and Innovation OfficeHungaryNKFI K 137793

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release