5KYV | pdb_00005kyv

Structure of Photinus pyralis Luciferase green shifted light emitting variant

• PDB DOI: https://doi.org/10.2210/pdb5KYV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Photinus pyralis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-07-22 Released: 2016-12-21 
• Deposition Author(s): Gulick, A.M.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Cloning of the Orange Light-Producing Luciferase from Photinus scintillans Provides Insight into Bioluminescence Color Determination

Branchini, B.R., Southworth, T.L., Fontaine, D.M., Murtiashaw, M.H., McGurk, A., Qureshi, R., Yetil, D., Sundlov, J.A., Gulick, A.M.

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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 122.94 kDa 
• Atom Count: 8,314 
• Modeled Residue Count: 1,073 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Luciferin 4-monooxygenase	A, B	550	Photinus pyralis	Mutation(s): 3  EC: 1.13.12.7
UniProt
Find proteins for P08659 (Photinus pyralis) Explore P08659  Go to UniProtKB:  P08659

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SLU	C [auth A], E [auth B]	5'-O-[N-(DEHYDROLUCIFERYL)-SULFAMOYL] ADENOSINE C21 H18 N8 O8 S3 LJLYTUYNVSHXQB-SOONXTGKSA-N
TLA	D [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.078	α = 90
b = 93.078	β = 90
c = 293.645	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Gulick, A.M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1410390
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116957

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description