5D9C

Luciferin-regenerating enzyme solved by SIRAS using XFEL (refined against Hg derivative data)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography.

Yamashita, K.Pan, D.Okuda, T.Sugahara, M.Kodan, A.Yamaguchi, T.Murai, T.Gomi, K.Kajiyama, N.Mizohata, E.Suzuki, M.Nango, E.Tono, K.Joti, Y.Kameshima, T.Park, J.Song, C.Hatsui, T.Yabashi, M.Iwata, S.Kato, H.Ago, H.Yamamoto, M.Nakatsu, T.

(2015) Sci Rep 5: 14017-14017

  • DOI: https://doi.org/10.1038/srep14017
  • Primary Citation of Related Structures:  
    5D9B, 5D9C, 5D9D

  • PubMed Abstract: 

    Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) holds great potential for structure determination of challenging proteins that are not amenable to producing large well diffracting crystals. Efficient de novo phasing methods are highly demanding and as such most SFX structures have been determined by molecular replacement methods. Here we employed single isomorphous replacement with anomalous scattering (SIRAS) for phasing and demonstrate successful application to SFX de novo phasing. Only about 20,000 patterns in total were needed for SIRAS phasing while single wavelength anomalous dispersion (SAD) phasing was unsuccessful with more than 80,000 patterns of derivative crystals. We employed high energy X-rays from SACLA (12.6 keV) to take advantage of the large anomalous enhancement near the LIII absorption edge of Hg, which is one of the most widely used heavy atoms for phasing in conventional protein crystallography. Hard XFEL is of benefit for de novo phasing in the use of routinely used heavy atoms and high resolution data collection.


  • Organizational Affiliation

    RIKEN SPring-8 Center, Sayo, 679-5148, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Luciferin regenerating enzyme311Photinus pyralisMutation(s): 0 
UniProt
Find proteins for Q95YI4 (Photinus pyralis)
Explore Q95YI4 
Go to UniProtKB:  Q95YI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95YI4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.1α = 90
b = 77.5β = 90
c = 84.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SHELXDEphasing
CrystFELdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations