4TNL

1.8 A resolution room temperature structure of Thermolysin recorded using an XFEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.

Kern, J.Tran, R.Alonso-Mori, R.Koroidov, S.Echols, N.Hattne, J.Ibrahim, M.Gul, S.Laksmono, H.Sierra, R.G.Gildea, R.J.Han, G.Hellmich, J.Lassalle-Kaiser, B.Chatterjee, R.Brewster, A.S.Stan, C.A.Glockner, C.Lampe, A.DiFiore, D.Milathianaki, D.Fry, A.R.Seibert, M.M.Koglin, J.E.Gallo, E.Uhlig, J.Sokaras, D.Weng, T.C.Zwart, P.H.Skinner, D.E.Bogan, M.J.Messerschmidt, M.Glatzel, P.Williams, G.J.Boutet, S.Adams, P.D.Zouni, A.Messinger, J.Sauter, N.K.Bergmann, U.Yano, J.Yachandra, V.K.

(2014) Nat Commun 5: 4371-4371

  • DOI: https://doi.org/10.1038/ncomms5371
  • Primary Citation of Related Structures:  
    4TNH, 4TNI, 4TNJ, 4TNK, 4TNL

  • PubMed Abstract: 

    The dioxygen we breathe is formed by light-induced oxidation of water in photosystem II. O2 formation takes place at a catalytic manganese cluster within milliseconds after the photosystem II reaction centre is excited by three single-turnover flashes. Here we present combined X-ray emission spectra and diffraction data of 2-flash (2F) and 3-flash (3F) photosystem II samples, and of a transient 3F' state (250 μs after the third flash), collected under functional conditions using an X-ray free electron laser. The spectra show that the initial O-O bond formation, coupled to Mn reduction, does not yet occur within 250 μs after the third flash. Diffraction data of all states studied exhibit an anomalous scattering signal from Mn but show no significant structural changes at the present resolution of 4.5 Å. This study represents the initial frames in a molecular movie of the structural changes during the catalytic reaction in photosystem II.


  • Organizational Affiliation

    1] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [2] LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermolysin316Bacillus thermoproteolyticusMutation(s): 0 
EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.0407α = 90
b = 93.0407β = 90
c = 130.41γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2015-10-07
    Changes: Other
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description