6Q3T

Structure of Protease1 from Pyrococcus horikoshii at room temperature in ChipX microfluidic device


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.

de Wijn, R.Hennig, O.Roche, J.Engilberge, S.Rollet, K.Fernandez-Millan, P.Brillet, K.Betat, H.Morl, M.Roussel, A.Girard, E.Mueller-Dieckmann, C.Fox, G.C.Olieric, V.Gavira, J.A.Lorber, B.Sauter, C.

(2019) Iucrj 6: 454-464

  • DOI: 10.1107/S2052252519003622
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct o ...

    Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.


    Organizational Affiliation

    Architecture et Réactivité de l'ARN, UPR 9002, CNRS, Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 15 Rue René Descartes, 67084 Strasbourg, France.,Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France.,Institute for Biochemistry, Leipzig University, Bruederstrasse 34, 04103 Leipzig, Germany.,Laboratorio de Estudios Cristalográficos, IACT, CSIC-Universidad de Granada, Avenida Las Palmeras 4, 18100 Armilla, Granada, Spain.,Architecture et Fonction des Macromolécules Biologiques, UMR 7257 CNRS-Aix Marseille University, 163 Avenue de Luminy, 13288 Marseille, France.,Paul Scherrer Institute, Swiss Light Source, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland.,PROXIMA 2A beamline, Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin, 91192 Gif-sur-Yvette, France.,Structural Biology, European Synchrotron Radiation Facility, 38043 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deglycase PH1704
A, B, C
166Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)Mutation(s): 0 
EC: 3.5.1.124
Find proteins for O59413 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Go to UniProtKB:  O59413
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.163 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 125.560α = 90.00
b = 125.560β = 90.00
c = 133.870γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-LABX-0036_NETRNA
French National Research AgencyFranceANR-11-LABX-0057_MITOCROSS
French National Research AgencyFranceANR-13-BS07-0007-01

Revision History 

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-29
    Type: Data collection, Database references
  • Version 1.2: 2019-06-05
    Type: Data collection, Database references, Source and taxonomy, Structure summary