6GZP | pdb_00006gzp

Llama nanobody PorM_02 structure determined at room temperature by in-situ diffraction in ChipX microfluidic device

• PDB DOI: https://doi.org/10.2210/pdb6GZP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-04 Released: 2018-07-18 
• Deposition Author(s): Roche, J., Gaubert, A., Desmyter, A., De Wijn, R., Sauter, C., Roussel, A.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.211 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

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

• PubMed: 31098026 
• DOI: https://doi.org/10.1107/S2052252519003622
• Primary Citation Related Structures: 
  6GZP, 6HW1, 6IBP, 6IBQ, 6Q3T, 6Q52


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration, homology, mass spectrometry

Macromolecule Content 

• Total Structure Weight: 14.52 kDa 
• Atom Count: 978 
• Modeled Residue Count: 121 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	A	129	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.211 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.68	α = 90
b = 66.68	β = 90
c = 91.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Roche, J., Gaubert, A., Desmyter, A., De Wijn, R., Sauter, C., Roussel, A.

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Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2019-05-01
  Changes: Data collection, Database references, Experimental preparation, Structure summary
• Version 1.2: 2019-05-29
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary