5LWO

Structure of Spin-labelled T4 lysozyme mutant L115C-R119C-R1 at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.183 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Internal Dynamics of the 3-Pyrroline-N-Oxide Ring in Spin-Labeled Proteins.

Consentius, P.Loll, B.Gohlke, U.Alings, C.Muller, C.Muller, R.Teutloff, C.Heinemann, U.Kaupp, M.Wahl, M.C.Risse, T.

(2017) J Phys Chem Lett 8: 1113-1117

  • DOI: 10.1021/acs.jpclett.6b02971

  • PubMed Abstract: 
  • Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a la ...

    Site-directed spin labeling is a versatile tool to study structure as well as dynamics of proteins using EPR spectroscopy. Methanethiosulfonate (MTS) spin labels tethered through a disulfide linkage to an engineered cysteine residue were used in a large number of studies to extract structural as well as dynamic information on the protein from the rotational dynamics of the nitroxide moiety. The ring itself was always considered to be a rigid body. In this contribution, we present a combination of high-resolution X-ray crystallography and EPR spectroscopy of spin-labeled protein single crystals demonstrating that the nitroxide ring inverts fast at ambient temperature while exhibiting nonplanar conformations at low temperature. We have used quantum chemical calculations to explore the potential energy that determines the ring dynamics as well as the impact of the geometry on the magnetic parameters probed by EPR spectroscopy.


    Organizational Affiliation

    Institute of Chemistry and Biochemistry, Freie Universität Berlin , Takustraße 3, 14195 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endolysin
A
164Enterobacteria phage T4Mutations: R119C, C97A, C54T, I137R, R12G, T115C
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HED
Query on HED

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A
2-HYDROXYETHYL DISULFIDE
C4 H10 O2 S2
KYNFOMQIXZUKRK-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

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A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
RXR
Query on RXR

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A
[2,2,5,5-tetramethyl-3,4-bis(sulfanylmethyl)-2,5-dihydro-1H-pyrrol-1-yl]oxidanyl radical
3,4-bis(thiomethyl)-2,2,5,5-tetramethyl-1H-Pyrrol-1-yloxyl radical
C10 H18 N O S2
PZEXYXPQVHSRCF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.183 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.141 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 60.170α = 90.00
b = 60.170β = 90.00
c = 97.720γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-03-29
    Type: Database references