5MND | pdb_00005mnd

SFX structure of Cydia pomonella granulovirus using a double flow-focusing nozzle

• PDB DOI: https://doi.org/10.2210/pdb5MND/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Cydia pomonella granulosis virus (isolate Mexican)
• Mutation(s): No 


• Deposited: 2016-12-13 Released: 2017-03-29 
• Deposition Author(s): Oberthuer, D., Chapman, H., Doerner, K., Xavier, P.L.
• Funding Organization(s): BMBF, National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Double-flow focused liquid injector for efficient serial femtosecond crystallography.

Oberthuer, D., Knoska, J., Wiedorn, M.O., Beyerlein, K.R., Bushnell, D.A., Kovaleva, E.G., Heymann, M., Gumprecht, L., Kirian, R.A., Barty, A., Mariani, V., Tolstikova, A., Adriano, L., Awel, S., Barthelmess, M., Dorner, K., Xavier, P.L., Yefanov, O., James, D.R., Nelson, G., Wang, D., Calvey, G., Chen, Y., Schmidt, A., Szczepek, M., Frielingsdorf, S., Lenz, O., Snell, E., Robinson, P.J., Sarler, B., Belsak, G., Macek, M., Wilde, F., Aquila, A., Boutet, S., Liang, M., Hunter, M.S., Scheerer, P., Lipscomb, J.D., Weierstall, U., Kornberg, R.D., Spence, J.C., Pollack, L., Chapman, H.N., Bajt, S.

(2017) Sci Rep 7: 44628-44628

• PubMed: 28300169 
• DOI: https://doi.org/10.1038/srep44628
• Primary Citation Related Structures: 
  5MND, 5U5Q


• PubMed Abstract: 
  

  Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double-flow focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices [corrected].

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Organizational Affiliation: 
• Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.
Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Department of Structural Biology, Stanford University, School of Medicine, Stanford, California 94305, USA.
SSRL, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
Department of Physics, Arizona State University, Tempe, AZ, USA.
Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.
Centre for Ultrafast Imaging, Luruper Chaussee 149, 22761 Hamburg, Germany.
IMPRS-UFAST, Max-Planck Institute for the Structure and Dynamics of Matter, 22675 Hamburg, Germany.
School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.
Institut für Chemie, Sekr. PC14, Technische Universität Berlin, Straße des 17, Juni 135, 10623 Berlin, Germany.
Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, USA.
Laboratory for Multiphase Processes, University of Nova Gorica, Vipavska 13, SI-5000 Nova Gorica, Slovenia.
Laboratory for Simulation of Materials and Processes, Institute of Metals and Technology, Lepi pot 11, SI-1000 Ljubljana, Slovenia.
Helmholtz-Zentrum Geesthacht, Max-Planck-Straße 1, 21502 Geesthacht, Germany.
LCLS, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.
Department of Biochemistry, Molecular Biology &Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 28.78 kDa 
• Atom Count: 2,122 
• Modeled Residue Count: 243 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Granulin	A	243	Cydia pomonella granulosis virus (isolate Mexican)	Mutation(s): 0
UniProt
Find proteins for P87577 (Cydia pomonella granulosis virus (isolate Mexico/1963)) Explore P87577  Go to UniProtKB:  P87577

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: I 2 3

Unit Cell:

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

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Oberthuer, D., Chapman, H., Doerner, K., Xavier, P.L.

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Funding Organization	Location	Grant Number
BMBF	Germany	05E13GU1
BMBF	Germany	05K13GUK
BMBF	Germany	05K2012
National Science Foundation (NSF, United States)	United States	1231306).

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Advisory, Data collection
• Version 1.2: 2018-11-14
  Changes: Data collection
• Version 1.3: 2022-03-30
  Changes: Advisory, Author supporting evidence, Database references
• Version 1.4: 2024-01-17
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary