5NJR

Mix-and-diffuse serial synchrotron crystallography: structure of N,N',N''-Triacetylchitotriose bound to Lysozyme with 50s time-delay, phased with 4ET8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mix-and-diffuse serial synchrotron crystallography.

Beyerlein, K.R.Dierksmeyer, D.Mariani, V.Kuhn, M.Sarrou, I.Ottaviano, A.Awel, S.Knoska, J.Fuglerud, S.Jonsson, O.Stern, S.Wiedorn, M.O.Yefanov, O.Adriano, L.Bean, R.Burkhardt, A.Fischer, P.Heymann, M.Horke, D.A.Jungnickel, K.E.J.Kovaleva, E.Lorbeer, O.Metz, M.Meyer, J.Morgan, A.Pande, K.Panneerselvam, S.Seuring, C.Tolstikova, A.Lieske, J.Aplin, S.Roessle, M.White, T.A.Chapman, H.N.Meents, A.Oberthuer, D.

(2017) IUCrJ 4: 769-777

  • DOI: 10.1107/S2052252517013124
  • Primary Citation of Related Structures:  5NJP, 5NJQ, 5NJS

  • PubMed Abstract: 
  • Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron las ...

    Unravelling the interaction of biological macromolecules with ligands and substrates at high spatial and temporal resolution remains a major challenge in structural biology. The development of serial crystallography methods at X-ray free-electron lasers and subsequently at synchrotron light sources allows new approaches to tackle this challenge. Here, a new polyimide tape drive designed for mix-and-diffuse serial crystallography experiments is reported. The structure of lysozyme bound by the competitive inhibitor chitotriose was determined using this device in combination with microfluidic mixers. The electron densities obtained from mixing times of 2 and 50 s show clear binding of chitotriose to the enzyme at a high level of detail. The success of this approach shows the potential for high-throughput drug screening and even structural enzymology on short timescales at bright synchrotron light sources.


    Organizational Affiliation

    Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusGene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CTO
Query on CTO

Download SDF File 
Download CCD File 
A
TRIACETYLCHITOTRIOSE
CHITOTRIOSE
C24 H41 N3 O16
WZZVUHWLNMNWLW-VFCSDQTKSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.166 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.610α = 90.00
b = 79.610β = 90.00
c = 38.300γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Database references