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- PDB-8s0g: Crystal structure of Renilla reniformis luciferase-GFP BRET complex -

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Basic information

Entry
Database: PDB / ID: 8s0g
TitleCrystal structure of Renilla reniformis luciferase-GFP BRET complex
Components
  • Coelenterazine h 2-monooxygenase
  • Green fluorescent protein
KeywordsHYDROLASE / bioluminescence / luciferase / green fluorescent protein / BRET (bioluminescence resonance energy transfer) complex / coelenteramide emitter
Function / homology
Function and homology information


Renilla-type luciferase / Renilla-luciferin 2-monooxygenase activity / carboxy-lyase activity / bioluminescence / generation of precursor metabolites and energy / membrane
Similarity search - Function
: / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-CEI / Coelenterazine h 2-monooxygenase / Green fluorescent protein
Similarity search - Component
Biological speciesRenilla reniformis (sea pansy)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.378 Å
AuthorsMarek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA22-09853S Czech Republic
CitationJournal: To Be Published
Title: Crystal structure of Renilla luciferase variant RLuc8 complexed with Renilla GFP (macromolecular BRET complex)
Authors: Marek, M.
History
DepositionFeb 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein
C: Coelenterazine h 2-monooxygenase
D: Coelenterazine h 2-monooxygenase
E: Green fluorescent protein
F: Green fluorescent protein
G: Coelenterazine h 2-monooxygenase
H: Coelenterazine h 2-monooxygenase
I: Green fluorescent protein
J: Green fluorescent protein
K: Coelenterazine h 2-monooxygenase
L: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,47213
Polymers378,06012
Non-polymers4111
Water6,684371
1
A: Green fluorescent protein
B: Green fluorescent protein
C: Coelenterazine h 2-monooxygenase
D: Coelenterazine h 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)126,0204
Polymers126,0204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Green fluorescent protein
F: Green fluorescent protein
G: Coelenterazine h 2-monooxygenase
H: Coelenterazine h 2-monooxygenase


Theoretical massNumber of molelcules
Total (without water)126,0204
Polymers126,0204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Green fluorescent protein
J: Green fluorescent protein
K: Coelenterazine h 2-monooxygenase
L: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,4325
Polymers126,0204
Non-polymers4111
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.875, 96.875, 361.461
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Green fluorescent protein


Mass: 26017.758 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Renilla reniformis (sea pansy) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: Q963I9
#2: Protein
Coelenterazine h 2-monooxygenase / Renilla-luciferin 2-monooxygenase / Renilla-type luciferase


Mass: 36992.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Renilla reniformis (sea pansy) / Production host: Escherichia coli (E. coli) / References: UniProt: P27652, Renilla-type luciferase
#3: Chemical ChemComp-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE


Mass: 411.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium tartrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.378→48.437 Å / Num. obs: 152020 / % possible obs: 99.5 % / Redundancy: 4 % / CC1/2: 0.997 / Net I/σ(I): 9
Reflection shellResolution: 2.378→2.46 Å / Num. unique obs: 15053 / CC1/2: 0.482

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.378→48.437 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2813 7219 4.76 %
Rwork0.2198 --
obs0.2227 151773 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.378→48.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25902 0 157 371 26430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326801
X-RAY DIFFRACTIONf_angle_d0.68436231
X-RAY DIFFRACTIONf_dihedral_angle_d5.34216796
X-RAY DIFFRACTIONf_chiral_restr0.0473867
X-RAY DIFFRACTIONf_plane_restr0.0044632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3782-2.40520.41621990.37264625X-RAY DIFFRACTION94
2.4052-2.43350.39182570.34434816X-RAY DIFFRACTION100
2.4335-2.46310.39762940.33314766X-RAY DIFFRACTION100
2.4631-2.49430.36812530.32564812X-RAY DIFFRACTION100
2.4943-2.52710.39192380.33214800X-RAY DIFFRACTION100
2.5271-2.56180.42121990.32714918X-RAY DIFFRACTION100
2.5618-2.59840.38071970.32084819X-RAY DIFFRACTION100
2.5984-2.63710.41463000.3264805X-RAY DIFFRACTION100
2.6371-2.67830.41932240.32424835X-RAY DIFFRACTION100
2.6783-2.72230.39671900.29644834X-RAY DIFFRACTION100
2.7223-2.76920.33662400.28424917X-RAY DIFFRACTION100
2.7692-2.81950.4062750.29084732X-RAY DIFFRACTION100
2.8195-2.87380.37471990.29684867X-RAY DIFFRACTION100
2.8738-2.93240.35292430.29024909X-RAY DIFFRACTION100
2.9324-2.99620.33582280.27154796X-RAY DIFFRACTION100
2.9962-3.06590.32692560.26614791X-RAY DIFFRACTION100
3.0659-3.14250.31222300.2554880X-RAY DIFFRACTION100
3.1425-3.22750.31692400.2534893X-RAY DIFFRACTION100
3.2275-3.32240.31022480.2334760X-RAY DIFFRACTION100
3.3224-3.42960.30812180.22454869X-RAY DIFFRACTION100
3.4296-3.55220.30212660.22394817X-RAY DIFFRACTION100
3.5522-3.69430.30692810.22014769X-RAY DIFFRACTION100
3.6943-3.86240.24862500.19324841X-RAY DIFFRACTION99
3.8624-4.06590.25022120.17614867X-RAY DIFFRACTION100
4.0659-4.32050.24482790.16934732X-RAY DIFFRACTION100
4.3205-4.65390.19712660.15854833X-RAY DIFFRACTION99
4.6539-5.12180.21492210.15544834X-RAY DIFFRACTION100
5.1218-5.86180.2222720.17434770X-RAY DIFFRACTION100
5.8618-7.3810.24921990.19644888X-RAY DIFFRACTION100
7.381-48.4370.20412450.17814759X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.8244 Å / Origin y: 27.5361 Å / Origin z: -23.4952 Å
111213212223313233
T0.3247 Å20.0186 Å2-0.0006 Å2-0.2495 Å20.0117 Å2--0.2382 Å2
L0.0907 °20.0145 °2-0.0138 °2-0.04 °2-0.0461 °2--0.1477 °2
S-0.0199 Å °0.0028 Å °0.0061 Å °0.0103 Å °-0.0145 Å °-0.0009 Å °-0.0225 Å °-0.0176 Å °-0 Å °
Refinement TLS groupSelection details: all

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