6GWA | pdb_00006gwa

Concanavalin B structure determined with data from the EuXFEL, the first MHz free electron laser

• PDB DOI: https://doi.org/10.2210/pdb6GWA/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Canavalia ensiformis
• Mutation(s): No 


• Deposited: 2018-06-22 Released: 2018-09-05 
• Deposition Author(s): Gruenbein, M.L., Gorel, A., Stricker, M., Bean, R., Bielecki, J., Doerner, K., Hartmann, E., Hilpert, M., Kloos, M., Letrun, R., Sztuk-Dambietz, J., Mancuso, A., Meserschmidt, M., Nass-Kovacs, G., Ramilli, M., Roome, C.M., Sato, T., Doak, R.B., Shoeman, R.L., Foucar, L., Colletier, J.P., Barends, T.R.M., Stan, C., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Megahertz data collection from protein microcrystals at an X-ray free-electron laser.

Grunbein, M.L., Bielecki, J., Gorel, A., Stricker, M., Bean, R., Cammarata, M., Dorner, K., Frohlich, L., Hartmann, E., Hauf, S., Hilpert, M., Kim, Y., Kloos, M., Letrun, R., Messerschmidt, M., Mills, G., Nass Kovacs, G., Ramilli, M., Roome, C.M., Sato, T., Scholz, M., Sliwa, M., Sztuk-Dambietz, J., Weik, M., Weinhausen, B., Al-Qudami, N., Boukhelef, D., Brockhauser, S., Ehsan, W., Emons, M., Esenov, S., Fangohr, H., Kaukher, A., Kluyver, T., Lederer, M., Maia, L., Manetti, M., Michelat, T., Munnich, A., Pallas, F., Palmer, G., Previtali, G., Raab, N., Silenzi, A., Szuba, J., Venkatesan, S., Wrona, K., Zhu, J., Doak, R.B., Shoeman, R.L., Foucar, L., Colletier, J.P., Mancuso, A.P., Barends, T.R.M., Stan, C.A., Schlichting, I.

(2018) Nat Commun 9: 3487-3487

• PubMed: 30154468 
• DOI: https://doi.org/10.1038/s41467-018-05953-4
• Primary Citation Related Structures: 
  6GW9, 6GWA, 6H0K, 6H0L


• PubMed Abstract: 
  

  X-ray free-electron lasers (XFELs) enable novel experiments because of their high peak brilliance and femtosecond pulse duration. However, non-superconducting XFELs offer repetition rates of only 10-120 Hz, placing significant demands on beam time and sample consumption. We describe serial femtosecond crystallography experiments performed at the European XFEL, the first MHz repetition rate XFEL, delivering 1.128 MHz X-ray pulse trains at 10 Hz. Given the short spacing between pulses, damage caused by shock waves launched by one XFEL pulse on sample probed by subsequent pulses is a concern. To investigate this issue, we collected data from lysozyme microcrystals, exposed to a ~15 μm XFEL beam. Under these conditions, data quality is independent of whether the first or subsequent pulses of the train were used for data collection. We also analyzed a mixture of microcrystals of jack bean proteins, from which the structure of native, magnesium-containing concanavalin A was determined.

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Organizational Affiliation: 
• Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany.
European XFEL GmbH, Holzkoppel 4, 22869, Schenefeld, Germany.
Department of Physics, UMR 625, UBL, University of Rennes 1, 35042, Rennes, France.
Deutsches Elektronensynchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.
BioXFEL STC, 700 Ellicott Street, Buffalo, NY, 14203, USA.
ARC Centre of Excellence for Advanced Molecular Imaging, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
Center for Free-Electron Laser Science, Deutsches Elektronensynchrotron, Notkestraße 85, 22607, Hamburg, Germany.
Laboratoire de Spectrochimie Infrarouge et Raman, CNRS, UMR 8516, Université de Lille, 59000, Lille, France.
Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.
Biological Research Centre (BRC), Hungarian Academy of Sciences, Temesvári krt. 62, Szeged, 6726, Hungary.
Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. [e-mail].
Department of Physics, Rutgers University Newark, 101 Warren Street, Newark, NJ, 07102, USA. [e-mail].
Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.87 kDa 
• Atom Count: 2,433 
• Modeled Residue Count: 283 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Concanavalin B	A	299	Canavalia ensiformis	Mutation(s): 0
UniProt
Find proteins for P49347 (Canavalia ensiformis) Explore P49347  Go to UniProtKB:  P49347

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.25	α = 90
b = 82.25	β = 90
c = 103.4	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Gruenbein, M.L., Gorel, A., Stricker, M., Bean, R., Bielecki, J., Doerner, K., Hartmann, E., Hilpert, M., Kloos, M., Letrun, R., Sztuk-Dambietz, J., Mancuso, A., Meserschmidt, M., Nass-Kovacs, G., Ramilli, M., Roome, C.M., Sato, T., Doak, R.B., Shoeman, R.L., Foucar, L., Colletier, J.P., Barends, T.R.M., Stan, C., Schlichting, I.

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2018-11-14
  Changes: Data collection
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary