5GTQ | pdb_00005gtq

Luciferin-regenerating enzyme at cryogenic temperature

• PDB DOI: https://doi.org/10.2210/pdb5GTQ/pdb

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


• Deposited: 2016-08-23 Released: 2016-11-09 
• Deposition Author(s): Yamashita, K., Murai, T., Yamamoto, M., Gomi, K., Kajiyama, N., Kato, H., Nakatsu, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free: 
  0.139 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.119 (Depositor) 

Starting Model: experimental

Literature

Luciferin-regenerating enzyme at cryogenic temperature

Yamashita, K.

To be published.

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: 34.96 kDa 
• Atom Count: 2,925 
• Modeled Residue Count: 307 
• 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 4 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], F [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.13 Å
• R-Value Free:  0.139 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.119 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.119 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.275	α = 90
b = 76.696	β = 90
c = 83.98	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Yamashita, K., Murai, T., Yamamoto, M., Gomi, K., Kajiyama, N., Kato, H., Nakatsu, T.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description