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- PDB-8aqi: NanoLuc luciferase with bound coelenteramide in surface allosteri... -

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Basic information

Entry
Database: PDB / ID: 8aqi
TitleNanoLuc luciferase with bound coelenteramide in surface allosteric site
ComponentsNanoLuc luciferase
KeywordsLUMINESCENT PROTEIN / Luciferase / NanoLuc / NLuc / luciferin / coelenterazine
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / Calycin / extracellular region / Chem-CEI / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 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
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)165,05128
Polymers163,1148
Non-polymers1,93720
Water6,125340
1
A: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8724
Polymers20,3891
Non-polymers4823
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)20,6193
Polymers20,3891
Non-polymers2302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 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
5
E: 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
6
F: 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
7
G: NanoLuc luciferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8363
Polymers20,3891
Non-polymers4472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: 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
Unit cell
Length a, b, c (Å)86.979, 87.282, 191.522
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-202-

CL

21G-342-

HOH

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Components

#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
#2: Chemical ChemComp-CEI / N-[3-BENZYL-5-(4-HYDROXYPHENYL)PYRAZIN-2-YL]-2-(4-HYDROXYPHENYL)ACETAMIDE / COELENTERAMIDE / Coelenteramide


Mass: 411.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
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: 44.81 %
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 twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.485
11-h,-k,l20.166
11-K, -H, -L30.18
11K, H, -L40.169
ReflectionResolution: 1.99→47.88 Å / Num. obs: 96944 / % possible obs: 98.9 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.7
Reflection shellResolution: 1.99→2.03 Å / Num. unique obs: 8970 / CC1/2: 0.36

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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: 8AQ6

8aq6


Resolution: 1.99→44.35 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.962 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0404 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 4918 5.1 %RANDOM
Rwork0.1884 ---
obs0.1894 91015 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.24 Å2 / Biso mean: 34.215 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1-3.73 Å2-0 Å24.15 Å2
2--12.55 Å20 Å2
3----16.28 Å2
Refinement stepCycle: final / Resolution: 1.99→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10816 0 116 340 11272
Biso mean--23.05 35.53 -
Num. residues----1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01311172
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710493
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.64115161
X-RAY DIFFRACTIONr_angle_other_deg1.3611.58724256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.60851366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32222.991565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.531151865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1471557
X-RAY DIFFRACTIONr_chiral_restr0.1030.21437
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022353
LS refinement shellResolution: 1.994→2.045 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.589 295 -
Rwork0.566 5783 -
all-6078 -
obs--84.91 %

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