5XFE | pdb_00005xfe

Luciferin-regenerating enzyme solved by SAD using XFEL (refined against 11,000 patterns)

• PDB DOI: https://doi.org/10.2210/pdb5XFE/pdb

• Classification: HYDROLASE
• Organism(s): Photinus pyralis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-10 Released: 2017-08-30 
• Deposition Author(s): Yamashita, K., Pan, D., Okuda, T., Murai, T., Kodan, A., Yamaguchi, T., Gomi, K., Kajiyama, N., Kato, H., Ago, H., Yamamoto, M., Nakatsu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography

Yamashita, K., Kuwabara, N., Nakane, T., Murai, T., Mizohata, E., Sugahara, M., Pan, D., Masuda, T., Suzuki, M., Sato, T., Kodan, A., Yamaguchi, T., Nango, E., Tanaka, T., Tono, K., Joti, Y., Kameshima, T., Hatsui, T., Yabashi, M., Manya, H., Endo, T., Kato, R., Senda, T., Kato, H., Iwata, S., Ago, H., Yamamoto, M., Yumoto, F., Nakatsu, T.

(2017) IUCrJ 4: 639-647

• PubMed: 28989719 
• DOI: https://doi.org/10.1107/S2052252517008557
• Primary Citation Related Structures: 
  5XFC, 5XFD, 5XFE


• PubMed Abstract: 
  

  Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) holds enormous potential for the structure determination of proteins for which it is difficult to produce large and high-quality crystals. SFX has been applied to various systems, but rarely to proteins that have previously unknown structures. Consequently, the majority of previously obtained SFX structures have been solved by the molecular replacement method. To facilitate protein structure determination by SFX, it is essential to establish phasing methods that work efficiently for SFX. Here, selenomethionine derivatization and mercury soaking have been investigated for SFX experiments using the high-energy XFEL at the SPring-8 Angstrom Compact Free-Electron Laser (SACLA), Hyogo, Japan. Three successful cases are reported of single-wavelength anomalous diffraction (SAD) phasing using X-rays of less than 1 Å wavelength with reasonable numbers of diffraction patterns (13 000, 60 000 and 11 000). It is demonstrated that the combination of high-energy X-rays from an XFEL and commonly used heavy-atom incorporation techniques will enable routine de novo structural determination of biomacromolecules.

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Organizational Affiliation: 
• RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, KEK/High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.
Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.
Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo 173-0015, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.

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: 34.75 kDa 
• Atom Count: 2,570 
• Modeled Residue Count: 306 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferin regenerating enzyme	A	311	Photinus pyralis	Mutation(s): 0  EC: 3.1.1.17
UniProt
Find proteins for Q95YI4 (Photinus pyralis) Explore Q95YI4  Go to UniProtKB:  Q95YI4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	B [auth A], C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1365656

Diffraction Data: https://doi.org/10.11577/1365655

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.9	α = 90
b = 77.03	β = 90
c = 84.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
SHELXDE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Yamashita, K., Pan, D., Okuda, T., Murai, T., Kodan, A., Yamaguchi, T., Gomi, K., Kajiyama, N., Kato, H., Ago, H., Yamamoto, M., Nakatsu, T.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2017-10-25
  Changes: Data collection, Database references
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations