4OW3

Thermolysin structure determined by free-electron laser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

Hattne, J.Echols, N.Tran, R.Kern, J.Gildea, R.J.Brewster, A.S.Alonso-Mori, R.Glockner, C.Hellmich, J.Laksmono, H.Sierra, R.G.Lassalle-Kaiser, B.Lampe, A.Han, G.Gul, S.DiFiore, D.Milathianaki, D.Fry, A.R.Miahnahri, A.White, W.E.Schafer, D.W.Seibert, M.M.Koglin, J.E.Sokaras, D.Weng, T.C.Sellberg, J.Latimer, M.J.Glatzel, P.Zwart, P.H.Grosse-Kunstleve, R.W.Bogan, M.J.Messerschmidt, M.Williams, G.J.Boutet, S.Messinger, J.Zouni, A.Yano, J.Bergmann, U.Yachandra, V.K.Adams, P.D.Sauter, N.K.

(2014) Nat.Methods 11: 545-548

  • DOI: 10.1038/nmeth.2887

  • PubMed Abstract: 
  • X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deri ...

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.


    Related Citations: 
    • New Python-based methods for data processing.
      Sauter, N.K.,Hattne, J.,Grosse-Kunstleve, R.W.,Echols, N.
      (2013) Acta Crystallogr. D Biol. Crystallogr. 69: 1274
    • Nanoflow electrospinning serial femtosecond crystallography.
      Sierra, R.G.,Laksmono, H.,Kern, J.,Tran, R.,Hattne, J.,Alonso-Mori, R.,Lassalle-Kaiser, B.,Glockner, C.,Hellmich, J.,Schafer, D.W.,Echols, N.,Gildea, R.J.,Grosse-Kunstleve, R.W.,Sellberg, J.,McQueen, T.A.,Fry, A.R.,Messerschmidt, M.M.,Miahnahri, A.,Seibert, M.M.,Hampton, C.Y.,Starodub, D.,Loh, N.D.,Sokaras, D.,Weng, T.C.,Zwart, P.H.,Glatzel, P.,Milathianaki, D.,White, W.E.,Adams, P.D.,Williams, G.J.,Boutet, S.,Zouni, A.,Messinger, J.,Sauter, N.K.,Bergmann, U.,Yano, J.,Yachandra, V.K.,Bogan, M.J.
      (2012) Acta Crystallogr. D Biol. Crystallogr. 68: 1584


    Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 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: 2.1 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.217 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.893α = 90.00
b = 92.893β = 90.00
c = 130.438γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM095887
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM102520
Department of Energy (United States)United StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM055302
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41GM103393

Revision History 

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-06-18
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2017-09-27
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary