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- PDB-8rzz: Crystal structure of Renilla luciferase RLuc8-GFP BRET complex at... -

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Basic information

Entry
Database: PDB / ID: 8rzz
TitleCrystal structure of Renilla luciferase RLuc8-GFP BRET complex at pH 9.0 (space group P32)
Components
  • Coelenterazine h 2-monooxygenase
  • Green fluorescent protein
KeywordsHYDROLASE / bioluminescence / luciferase / green fluorescent protein / coelenteramide
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: 2.299 Å
AuthorsMarek, M. / Smrckova, A.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science FoundationGA22-09853S Czech Republic
CitationJournal: To Be Published
Title: Crystal structure of Renilla luciferase RLuc8-GFP BRET complex at pH 9.0 (space group P32)
Authors: Marek, M. / Smrckova, A.
History
DepositionFeb 13, 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)380,11817
Polymers378,06012
Non-polymers2,0575
Water11,656647
1
A: Green fluorescent protein
B: Green fluorescent protein
C: Coelenterazine h 2-monooxygenase
D: 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
Buried area8990 Å2
ΔGint-45 kcal/mol
Surface area41140 Å2
MethodPISA
2
E: Green fluorescent protein
F: Green fluorescent protein
G: Coelenterazine h 2-monooxygenase
H: Coelenterazine h 2-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,8436
Polymers126,0204
Non-polymers8232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9900 Å2
ΔGint-59 kcal/mol
Surface area40970 Å2
MethodPISA
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)126,8436
Polymers126,0204
Non-polymers8232
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10170 Å2
ΔGint-55 kcal/mol
Surface area40350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.988, 97.988, 361.996
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.: 5 / Source method: obtained synthetically / Formula: C25H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: T-mate, Bicine, PEG Smear High, ethylene glycol

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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: 2.299→49.172 Å / Num. obs: 172869 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 0.997 / Net I/σ(I): 11
Reflection shellResolution: 2.299→2.42 Å / Num. unique obs: 25234 / CC1/2: 0.572

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→49.172 Å / Cross valid method: FREE R-VALUE / σ(F): 217.79 / Phase error: 41.34 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2565 8477 4.91 %
Rwork0.2267 --
obs0.2489 172762 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.299→49.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25916 0 317 647 26880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00227017
X-RAY DIFFRACTIONf_angle_d0.56336523
X-RAY DIFFRACTIONf_dihedral_angle_d4.58918380
X-RAY DIFFRACTIONf_chiral_restr0.0453878
X-RAY DIFFRACTIONf_plane_restr0.0044666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33970.40864140.35218273X-RAY DIFFRACTION95
2.3397-2.38220.38394560.34618127X-RAY DIFFRACTION95
2.3822-2.4280.38984040.34168176X-RAY DIFFRACTION95
2.428-2.47750.3634580.3448183X-RAY DIFFRACTION95
2.4775-2.53140.38923480.33638361X-RAY DIFFRACTION96
2.5314-2.59020.37124280.33178203X-RAY DIFFRACTION95
2.5902-2.6550.37223760.33168257X-RAY DIFFRACTION96
2.655-2.72670.39024340.31768182X-RAY DIFFRACTION95
2.7267-2.80690.354140.30958221X-RAY DIFFRACTION95
2.8069-2.89750.35914280.3088205X-RAY DIFFRACTION95
2.8975-3.0010.33534130.29448189X-RAY DIFFRACTION95
3.001-3.1210.31414940.27338156X-RAY DIFFRACTION94
3.121-3.26290.30154340.26368243X-RAY DIFFRACTION95
3.2629-3.43480.30414050.24818150X-RAY DIFFRACTION95
3.4348-3.64970.25984490.24268239X-RAY DIFFRACTION95
3.6497-3.9310.24533800.22768258X-RAY DIFFRACTION96
3.931-4.32570.24564200.20458171X-RAY DIFFRACTION95
4.3257-4.94970.21054480.1878182X-RAY DIFFRACTION95
4.9497-6.22850.22654210.20058198X-RAY DIFFRACTION95
6.2285-31.9520.23254520.20878208X-RAY DIFFRACTION95

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