6SRQ

X-ray pump X-ray probe on thaumatin nanocrystals: 18 fs time delay


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural dynamics in proteins induced by and probed with X-ray free-electron laser pulses.

Nass, K.Gorel, A.Abdullah, M.M.V Martin, A.Kloos, M.Marinelli, A.Aquila, A.Barends, T.R.M.Decker, F.J.Bruce Doak, R.Foucar, L.Hartmann, E.Hilpert, M.Hunter, M.S.Jurek, Z.Koglin, J.E.Kozlov, A.Lutman, A.A.Kovacs, G.N.Roome, C.M.Shoeman, R.L.Santra, R.Quiney, H.M.Ziaja, B.Boutet, S.Schlichting, I.

(2020) Nat Commun 11: 1814-1814

  • DOI: 10.1038/s41467-020-15610-4
  • Primary Citation of Related Structures:  
    6SR0, 6SR1, 6SR2, 6SR3, 6SR4, 6SR5, 6SRJ, 6SRK, 6SRL, 6SRO, 6SRP, 6SRQ

  • PubMed Abstract: 
  • X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples ...

    X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter's correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.


    Organizational Affiliation

    Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany. ilme.schlichting@mpimf-heidelberg.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thaumatin-1A207Thaumatococcus danielliiMutation(s): 0 
UniProt
Find proteins for P02883 (Thaumatococcus daniellii)
Explore P02883 
Go to UniProtKB:  P02883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02883
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download Ideal Coordinates CCD File 
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.849α = 90
b = 57.849β = 90
c = 150.328γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release