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- PDB-8aq6: NanoLuc luciferase with bound furimamide in surface allosteric site -

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Basic information

Entry
Database: PDB / ID: 8aq6
TitleNanoLuc luciferase with bound furimamide in surface allosteric site
ComponentsNanoLuc luciferase
KeywordsLUMINESCENT PROTEIN / Luciferase / NanoLuc / NLuc / luciferin / furimazine
Function / homology
Function and homology information


Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / extracellular region
Similarity search - Function
Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-NT0 / OXYGEN MOLECULE / TRIETHYLENE GLYCOL / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Similarity search - Component
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 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 11, 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
C: NanoLuc luciferase
D: NanoLuc luciferase
E: NanoLuc luciferase
F: NanoLuc luciferase
G: NanoLuc luciferase
H: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,98942
Polymers163,1148
Non-polymers2,87534
Water13,872770
1
A: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2029
Polymers20,3891
Non-polymers8138
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6905
Polymers20,3891
Non-polymers3014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6544
Polymers20,3891
Non-polymers2653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6104
Polymers20,3891
Non-polymers2213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9207
Polymers20,3891
Non-polymers5306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4603
Polymers20,3891
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9006
Polymers20,3891
Non-polymers5115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5524
Polymers20,3891
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.910, 87.489, 191.761
Angle α, β, γ (deg.)90.000, 90.090, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-402-

CL

21C-202-

CL

31C-368-

HOH

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 20389.240 Da / Num. of mol.: 8
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

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Non-polymers , 7 types, 804 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NT0 / N-(3-Benzyl-5-phenylpyrazin-2-yl)-2-(furan-2-yl)acetamide / 2-(furan-2-yl)-~{N}-[5-phenyl-3-(phenylmethyl)pyrazin-2-yl]ethanamide


Mass: 369.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 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: 0.9999 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.606
11h,-k,-l20.214
11K, H, -L30.089
11-K, -H, -L40.09
ReflectionResolution: 1.69→47.94 Å / Num. obs: 158483 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.7
Reflection shellResolution: 1.69→1.73 Å / Num. unique obs: 14059 / CC1/2: 0.503

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B0U

5b0u


Resolution: 1.69→47.94 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.232 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1827 7979 5.1 %RANDOM
Rwork0.1345 ---
obs0.1369 148996 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.07 Å2 / Biso mean: 31.334 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å2-0 Å22.26 Å2
2--9.89 Å20 Å2
3----12.43 Å2
Refinement stepCycle: final / Resolution: 1.69→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10800 0 165 771 11736
Biso mean--40.81 39.45 -
Num. residues----1369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01311197
X-RAY DIFFRACTIONr_bond_other_d0.0030.01710560
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.6415169
X-RAY DIFFRACTIONr_angle_other_deg1.3971.59424426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.70651369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05622.966563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.17151863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9481557
X-RAY DIFFRACTIONr_chiral_restr0.1450.21437
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212452
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022341
X-RAY DIFFRACTIONr_rigid_bond_restr6.413321757
LS refinement shellResolution: 1.69→1.733 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.518 428 -
Rwork0.412 8452 -
obs--74.96 %

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