7OMR | pdb_00007omr

Crystal structure of coelenteramide-bound Renilla reniformis luciferase RLuc8-D162A variant

• PDB DOI: https://doi.org/10.2210/pdb7OMR/pdb

• Classification: LUMINESCENT PROTEIN
• Organism(s): Renilla reniformis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-05-24 Released: 2022-06-01 
• Deposition Author(s): Schenkmayerova, A., Marek, M.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.164 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Catalytic mechanism for Renilla-type luciferases

Schenkmayerova, A., Toul, M., Pluskal, D., Baatallah, R., Gagnot, G., Pinto, G.P., Santana, V.T., Stuchla, M., Neugebauer, P., Chaiyen, P., Damborsky, J., Bednar, D., Janin, Y.L., Prokop, Z., Marek, M.

(2023) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-022-00895-z

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.68 kDa 
• Atom Count: 2,962 
• Modeled Residue Count: 309 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coelenterazine h 2-monooxygenase	A	317	Renilla reniformis	Mutation(s): 1  EC: 1.13.12.5
UniProt
Find proteins for P27652 (Renilla reniformis) Explore P27652  Go to UniProtKB:  P27652

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CEI (Subject of Investigation/LOI)	B [auth A]	N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE C25 H21 N3 O3 CJIIERPDFZUYPI-UHFFFAOYSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.186 (Depositor), 0.164 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.445	α = 90
b = 74.166	β = 90
c = 80.346	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Schenkmayerova, A., Marek, M.

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Funding Organization	Location	Grant Number
European Commission	Czech Republic	MSCA-IF-2017 792772

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2023-01-18
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description