8S0G | pdb_00008s0g

Crystal structure of Renilla reniformis luciferase-GFP BRET complex

PDB DOI: https://doi.org/10.2210/pdb8S0G/pdb

Classification: HYDROLASE
Organism(s): Renilla reniformis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-02-14 Released: 2025-09-03
Deposition Author(s): Marek, M.
Funding Organization(s): Czech Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.281 (Depositor), 0.283 (DCC)
R-Value Work:
0.220 (Depositor), 0.224 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Renilla luciferase variant RLuc8 complexed with Renilla GFP (macromolecular BRET complex)

Marek, M.

To be published.

Macromolecule Content

Total Structure Weight: 378.47 kDa
Atom Count: 26,441
Modeled Residue Count: 3,224
Deposited Residue Count: 3,300
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B, E, F, I A, B, E, F, I, J	231	Renilla reniformis	Mutation(s): 1 Gene Names: GFP
UniProt
Find proteins for Q963I9 (Renilla reniformis) Explore Q963I9 Go to UniProtKB: Q963I9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q963I9
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coelenterazine h 2-monooxygenase	C, D, G, H, K C, D, G, H, K, L	319	Renilla reniformis	Mutation(s): 8 EC: 1.13.12.5
UniProt
Find proteins for P27652 (Renilla reniformis) Explore P27652 Go to UniProtKB: P27652
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27652
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CEI (Subject of Investigation/LOI) Query on CEI Download Ideal Coordinates CCD File SDF format, chain M [auth L] MOL2 format, chain M [auth L] mmCIF format, chain M [auth L]	M [auth L]	N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE C₂₅ H₂₁ N₃ O₃ CJIIERPDFZUYPI-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRO Query on CRO	A, B, E, F, I A, B, E, F, I, J	L-PEPTIDE LINKING	C₁₅ H₁₇ N₃ O₅		THR, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.281 (Depositor), 0.283 (DCC)
R-Value Work: 0.220 (Depositor), 0.224 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.875	α = 90
b = 96.875	β = 90
c = 361.461	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALA	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	GA22-09853S

Revision History (Full details and data files)

Version 1.0: 2025-09-03
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.