5NJS

Mix-and-diffuse serial synchrotron crystallography: structure of N,N',N''-Triacetylchitotriose bound to Lysozyme with 50s time-delay, phased with 1HEW


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5NJR - determined by Oberthuer, D., Meents, A., Beyerlein, K.R., Chapman, H.N., Lieseke, J.  

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, 5NJR

  • 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
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
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.164 
  • 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
CrystFELdata scaling
CrystFELdata reduction
PHENIXrefinement
PHENIXphasing

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