200us Temperature-Jump (Light) XFEL structure of Lysozyme

Experimental Data Snapshot

  • Resolution: 1.57 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography.

Wolff, A.M.Nango, E.Young, I.D.Brewster, A.S.Kubo, M.Nomura, T.Sugahara, M.Owada, S.Barad, B.A.Ito, K.Bhowmick, A.Carbajo, S.Hino, T.Holton, J.M.Im, D.O'Riordan, L.J.Tanaka, T.Tanaka, R.Sierra, R.G.Yumoto, F.Tono, K.Iwata, S.Sauter, N.K.Fraser, J.S.Thompson, M.C.

(2023) Nat Chem 15: 1549-1558

  • DOI: https://doi.org/10.1038/s41557-023-01329-4
  • Primary Citation of Related Structures:  
    8CVU, 8CVV, 8CVW, 8CW0, 8CW1, 8CW3, 8CW5, 8CW6, 8CW7, 8CW8, 8CWB, 8CWC, 8CWD, 8CWE, 8CWF, 8CWG, 8CWH

  • PubMed Abstract: 

    Understanding and controlling protein motion at atomic resolution is a hallmark challenge for structural biologists and protein engineers because conformational dynamics are essential for complex functions such as enzyme catalysis and allosteric regulation. Time-resolved crystallography offers a window into protein motions, yet without a universal perturbation to initiate conformational changes the method has been limited in scope. Here we couple a solvent-based temperature jump with time-resolved crystallography to visualize structural motions in lysozyme, a dynamic enzyme. We observed widespread atomic vibrations on the nanosecond timescale, which evolve on the submillisecond timescale into localized structural fluctuations that are coupled to the active site. An orthogonal perturbation to the enzyme, inhibitor binding, altered these dynamics by blocking key motions that allow energy to dissipate from vibrations into functional movements linked to the catalytic cycle. Because temperature jump is a universal method for perturbing molecular motion, the method demonstrated here is broadly applicable for studying protein dynamics.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.511α = 90
b = 79.511β = 90
c = 38.192γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
cxi.mergedata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1231306
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Refinement description
  • Version 1.4: 2023-11-15
    Changes: Database references