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Phycocyanin structure from T. elongatus at 2.5-A from XFEL using a viscous delivery medium for serial femtosecond crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel inert crystal delivery medium for serial femtosecond crystallography.

Conrad, C.E.Basu, S.James, D.Wang, D.Schaffer, A.Roy-Chowdhury, S.Zatsepin, N.A.Aquila, A.Coe, J.Gati, C.Hunter, M.S.Koglin, J.E.Kupitz, C.Nelson, G.Subramanian, G.White, T.A.Zhao, Y.Zook, J.Boutet, S.Cherezov, V.Spence, J.C.Fromme, R.Weierstall, U.Fromme, P.

(2015) Iucrj 2: 421-430

  • DOI: 10.1107/S2052252515009811

  • PubMed Abstract: 
  • Serial femtosecond crystallography (SFX) has opened a new era in crystallo-graphy by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron la ...

    Serial femtosecond crystallography (SFX) has opened a new era in crystallo-graphy by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.


    Organizational Affiliation

    Center for Applied Structural Discovery, The Biodesign Institute , PO Box 875001, Tempe, AZ 85287-5001, USA ; Department of Physics, Arizona State University , PO Box 871604, Tempe, AZ 85287-1504, USA.,Department of Physics, Arizona State University , PO Box 871604, Tempe, AZ 85287-1504, USA.,Center for Applied Structural Discovery, The Biodesign Institute , PO Box 875001, Tempe, AZ 85287-5001, USA ; Department of Physics, University of Wisconsin-Milwaukee , 1900 East Kenwood Boulevard, Milwaukee, WI 53211, USA.,Department of Chemistry and Biochemistry, Arizona State University , PO Box 871604, Tempe, AZ 85287-1604, USA ; Center for Applied Structural Discovery, The Biodesign Institute , PO Box 875001, Tempe, AZ 85287-5001, USA.,SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.,Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY , Notkestrasse 85, 22607 Hamburg, Germany.,Bridge Institute, Department of Chemistry, University of Southern California , 3430 S. Vermont Avenue, Los Angeles, CA 90089, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-phycocyanin alpha chain
A
162Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: cpcA
Find proteins for P50032 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P50032
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-phycocyanin beta chain
B
172Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: cpcB
Find proteins for P50033 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P50033
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYC
Query on CYC

Download SDF File 
Download CCD File 
A, B
PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEN
Query on MEN
B
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.187 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 153.400α = 90.00
b = 153.400β = 90.00
c = 39.640γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health Femtosecond Nano- crystallography of Membrane Proteins AwardUnited States617095583
National Institutes of Health/National Institute of General Medical SciencesUnited StatesU54GM094599
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM108635
Department of Energy (United States)United StatesDE-SC001057
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM097463

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-09-19
    Type: Data collection