4TNL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1038/ncomms5371
  • Primary Citation of Related Structures:  

  • 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 flashe ...

    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.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V.,Grosse-Kunstleve, R.W.,Echols, N.,Headd, J.J.,Moriarty, N.W.,Mustyakimov, M.,Terwilliger, T.C.,Urzhumtsev, A.,Zwart, P.H.,Adams, P.D.
      (2012) Acta Crystallogr. D Biol. Crystallogr. 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D.,Afonine, P.V.,Bunkoczi, G.,Chen, V.B.,Davis, I.W.,Echols, N.,Headd, J.J.,Hung, L.W.,Kapral, G.J.,Grosse-Kunstleve, R.W.,McCoy, A.J.,Moriarty, N.W.,Oeffner, R.,Read, R.J.,Richardson, D.C.,Richardson, J.S.,Terwilliger, T.C.,Zwart, P.H.
      (2010) Acta Crystallogr. D Biol. Crystallogr. 66: 213


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermolysin
A
316Bacillus thermoproteolyticusMutation(s): 0 
Gene Names: npr
EC: 3.4.24.27
Find proteins for P00800 (Bacillus thermoproteolyticus)
Go to UniProtKB:  P00800
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.212 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.041α = 90.00
b = 93.041β = 90.00
c = 130.410γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
cctbx.xfeldata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2015-10-07
    Type: Other