Photoactive Yellow Protein PYP Dark Full

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Time-resolved serial femtosecond crystallography at the European XFEL.

Pandey, S.Bean, R.Sato, T.Poudyal, I.Bielecki, J.Cruz Villarreal, J.Yefanov, O.Mariani, V.White, T.A.Kupitz, C.Hunter, M.Abdellatif, M.H.Bajt, S.Bondar, V.Echelmeier, A.Doppler, D.Emons, M.Frank, M.Fromme, R.Gevorkov, Y.Giovanetti, G.Jiang, M.Kim, D.Kim, Y.Kirkwood, H.Klimovskaia, A.Knoska, J.Koua, F.H.M.Letrun, R.Lisova, S.Maia, L.Mazalova, V.Meza, D.Michelat, T.Ourmazd, A.Palmer, G.Ramilli, M.Schubert, R.Schwander, P.Silenzi, A.Sztuk-Dambietz, J.Tolstikova, A.Chapman, H.N.Ros, A.Barty, A.Fromme, P.Mancuso, A.P.Schmidt, M.

(2020) Nat Methods 17: 73-78

  • DOI: https://doi.org/10.1038/s41592-019-0628-z
  • Primary Citation of Related Structures:  
    6P4I, 6P5D, 6P5E, 6P5F, 6P5G

  • PubMed Abstract: 

    The European XFEL (EuXFEL) is a 3.4-km long X-ray source, which produces femtosecond, ultrabrilliant and spatially coherent X-ray pulses at megahertz (MHz) repetition rates. This X-ray source has been designed to enable the observation of ultrafast processes with near-atomic spatial resolution. Time-resolved crystallographic investigations on biological macromolecules belong to an important class of experiments that explore fundamental and functional structural displacements in these molecules. Due to the unusual MHz X-ray pulse structure at the EuXFEL, these experiments are challenging. Here, we demonstrate how a biological reaction can be followed on ultrafast timescales at the EuXFEL. We investigate the picosecond time range in the photocycle of photoactive yellow protein (PYP) with MHz X-ray pulse rates. We show that difference electron density maps of excellent quality can be obtained. The results connect the previously explored femtosecond PYP dynamics to timescales accessible at synchrotrons. This opens the door to a wide range of time-resolved studies at the EuXFEL.

  • Organizational Affiliation

    Physics Department, University of Wisconsin-Milwaukee, Milwaukee, WI, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photoactive yellow protein125Halorhodospira halophilaMutation(s): 0 
Gene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16113
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on 60F
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 63
  • Diffraction Data: https://doi.org/10.11577/1577287
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.9α = 90
b = 66.9β = 90
c = 40.8γ = 120
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1231306

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.2: 2019-12-04
    Changes: Database references
  • Version 1.3: 2020-01-15
    Changes: Database references
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references
  • Version 1.5: 2023-11-15
    Changes: Data collection, Derived calculations