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- PDB-8aqh: NanoLuc-Y94A luciferase mutant -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8aqh
TitleNanoLuc-Y94A luciferase mutant
ComponentsNanoLuc luciferase
KeywordsLUMINESCENT PROTEIN / Luciferase / NanoLuc / NLuc / luciferin / furimazine
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / Calycin / extracellular region / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.798 Å
AuthorsNemergut, M. / Marek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Science Foundation22-09853S Czech Republic
CitationJournal: Nat Commun / Year: 2023
Title: Illuminating the mechanism and allosteric behavior of NanoLuc luciferase.
Authors: Nemergut, M. / Pluskal, D. / Horackova, J. / Sustrova, T. / Tulis, J. / Barta, T. / Baatallah, R. / Gagnot, G. / Novakova, V. / Majerova, M. / Sedlackova, K. / Marques, S.M. / Toul, M. / ...Authors: Nemergut, M. / Pluskal, D. / Horackova, J. / Sustrova, T. / Tulis, J. / Barta, T. / Baatallah, R. / Gagnot, G. / Novakova, V. / Majerova, M. / Sedlackova, K. / Marques, S.M. / Toul, M. / Damborsky, J. / Prokop, Z. / Bednar, D. / Janin, Y.L. / Marek, M.
History
DepositionAug 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NanoLuc luciferase
B: NanoLuc luciferase


Theoretical massNumber of molelcules
Total (without water)40,5942
Polymers40,5942
Non-polymers00
Water28816
1
A: NanoLuc luciferase


Theoretical massNumber of molelcules
Total (without water)20,2971
Polymers20,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NanoLuc luciferase


Theoretical massNumber of molelcules
Total (without water)20,2971
Polymers20,2971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.449, 86.473, 96.237
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein NanoLuc luciferase / 19kOLase / Oplophorus-luciferin 2-monooxygenase catalytic subunit


Mass: 20297.143 Da / Num. of mol.: 2 / Mutation: Y94A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oplophorus gracilirostris (crustacean)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: MgCl2, KCl, Na acetate, PEG-400

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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 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.5
ReflectionResolution: 2.798→48.12 Å / Num. obs: 9193 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 10.6
Reflection shellResolution: 2.798→2.95 Å / Num. unique obs: 897 / CC1/2: 0.28

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AQ6

8aq6


Resolution: 2.798→43.224 Å / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.28 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3048 430 4.68 %
Rwork0.2614 8690 -
obs0.2762 9193 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.41 Å2 / Biso mean: 67.2789 Å2 / Biso min: 21.93 Å2
Refinement stepCycle: final / Resolution: 2.798→43.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 0 16 2702
Biso mean---40.75 -
Num. residues----342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8064-3.21210.3821510.34042848299995
3.2121-4.04510.37141140.2942872298696
4.0451-29.13570.27831650.25112970313595

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