4Z8K

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: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1107/S2052252515009811
  • Primary Citation of Related Structures:  
    4Z8K

  • 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 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

    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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin alpha chain162Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50032 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50032 
Go to UniProtKB:  P50032
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50032
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-phycocyanin beta chain172Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P50033 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P50033 
Go to UniProtKB:  P50033
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50033
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEN
Query on MEN
B
L-PEPTIDE LINKINGC5 H10 N2 O3ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.191 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.4α = 90
b = 153.4β = 90
c = 39.64γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM095583
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54GM094599
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM108635
Department of Energy (DOE, United States)United StatesDE-SC001057
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097463

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.2: 2018-09-19
    Changes: Data collection
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2022-03-23
    Changes: Author supporting evidence, Database references
  • Version 1.5: 2023-09-27
    Changes: Data collection, Refinement description