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- PDB-7snt: 2.20A Resolution Structure of NanoLuc Luciferase with Bound Subst... -

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Basic information

Entry
Database: PDB / ID: 7snt
Title2.20A Resolution Structure of NanoLuc Luciferase with Bound Substrate Analog 3-methoxy-furimazine
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsOXIDOREDUCTASE / OPLOPHORUS BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE / NLUC / COELENTERAZINE / FURIMAZINE / BETA-BARREL / 3-methoxy-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-9Z5 / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Similarity search - Component
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Unch, J. / Encell, L.P. / Wood, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: 2.20A Resolution Structure of NanoLuc Luciferase with Bound Substrate Analog 3-methoxy-furimazine
Authors: Encell, L.P. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Wood, K.V.
History
DepositionOct 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2543
Polymers38,8582
Non-polymers3951
Water1,18966
1
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8252
Polymers19,4291
Non-polymers3951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)19,4291
Polymers19,4291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.648, 61.249, 64.664
Angle α, β, γ (deg.)90.000, 102.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 19429.164 Da / Num. of mol.: 2
Mutation: A4E, Q11R, Q18L, L27V, A33N, K43R, V44I, A54I, F68D, L72Q, M75K, I90V, P115E, Q124K, Y138I, N166R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oplophorus gracilirostris (crustacean) / Plasmid: PFN18K(-AIA) / Production host: Escherichia coli KRX (bacteria)
References: UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase
#2: Chemical ChemComp-9Z5 / (4S)-8-benzyl-2-[(furan-2-yl)methyl]-3-methoxy-6-phenylimidazo[1,2-a]pyrazine


Mass: 395.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.33 Å3/Da / Density % sol: 47.3 % / Mosaicity: 0.26 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M sodium citrate dibasic, 0.1 M Tris, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→45.79 Å / Num. obs: 18190 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.54 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.058 / Rrim(I) all: 0.107 / Net I/σ(I): 9.4 / Num. measured all: 61036
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.270.625532815750.7740.3990.744298.9
9.07-45.790.049462810.9940.0270.04925.298.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.12 Å42.12 Å
Translation3.12 Å42.12 Å

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Processing

Software
NameVersionClassification
PHENIXdev_4289refinement
XDSdata reduction
Aimless0.1.29data scaling
PHASER2.5.4phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBO

5ibo


Resolution: 2.2→42.12 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.02 / Phase error: 29.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 932 5.12 %
Rwork0.2106 17255 -
obs0.2134 18187 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.31 Å2 / Biso mean: 42.1205 Å2 / Biso min: 17.81 Å2
Refinement stepCycle: final / Resolution: 2.2→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 30 66 2404
Biso mean--39.63 36.86 -
Num. residues----297
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.320.31291420.24132452259499
2.32-2.460.31691310.24152416254799
2.46-2.650.29511330.23282449258299
2.65-2.920.30461300.217724662596100
2.92-3.340.29091320.21552450258299
3.34-4.210.24261370.18732473261099
4.21-42.120.22431270.20552549267699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3334-0.57831.13811.55490.59581.7227-0.0212-0.18090.1610.1476-0.0894-0.1571-0.15570.10160.00010.19010.00210.01340.2522-0.00460.2551-12.0435-18.75335.4826
20.5502-0.14860.28511.4747-0.57072.74420.0243-0.10150.39440.6840.1024-0.7628-0.55890.0818-0.0660.40230.07860.02250.2963-0.10.6217-11.9122-4.489213.7235
30.31350.4644-0.49840.5078-0.59980.6006-0.14740.03320.05990.06570.14720.2721-0.0576-0.0616-00.14820.0180.01230.2114-0.02060.2947-23.6256-19.70591.0303
40.33750.53050.48420.64210.34941.48450.02920.03970.0276-0.0516-0.0745-0.00540.22030.12680.00010.20930.0360.01220.2229-0.00070.221-12.128-20.4164-1.4973
50.40130.109-0.51910.7195-0.57580.725-0.10560.11950.0981-0.0069-0.08040.4804-0.14-0.429600.4630.0221-0.00370.4085-0.03810.36636.7277-18.355221.3212
65.81030.5436-0.69550.25690.13530.2775-0.0784-0.40070.5235-0.2138-0.1121-0.21650.35570.3857-0.1220.7870.13510.05750.28780.01380.274916.6635-36.375616.0875
70.6268-0.2613-1.05011.4408-1.20773.7359-0.4314-0.1806-0.9063-0.87960.62770.43351.1359-1.36070.08110.88510.04930.13640.5973-0.03610.65028.9796-38.661217.7422
80.065-0.44840.11543.234-0.92920.27320.4464-0.51330.82471.4617-0.3875-0.145-0.4716-0.257-0.01310.4694-0.04960.08050.5145-0.0310.30734.5296-20.718631.4883
90.21950.06190.20143.1380.10711.50970.1692-0.44810.24071.26580.00990.5713-0.8844-0.16030.10950.47120.00920.03640.47740.12740.2658.5101-29.176531.1806
100.6695-0.0323-0.34930.0120.04230.40160.2374-0.4198-0.06270.51-0.4814-0.5208-0.02970.6296-0.0070.5509-0.0214-0.1750.55410.04640.356718.0711-24.354929.9398
110.5785-0.67820.37571.1491-0.46320.3301-0.0459-0.34090.26310.46650.0963-0.51370.05260.14370.01920.35560.0499-0.02170.34230.04010.29716.6845-26.032622.0517
121.7149-1.6086-0.89682.24890.41680.4763-0.35290.1293-0.4749-0.10360.21440.21070.89520.12260.2320.24740.04990.08650.27830.03470.13678.6333-23.892316.5971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 59 )A-1 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 92 )A60 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 130 )A93 - 130
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 167 )A131 - 167
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 16 )B-1 - 16
6X-RAY DIFFRACTION6chain 'B' and (resid 17 through 24 )B17 - 24
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 40 )B25 - 40
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 50 )B41 - 50
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 111 )B51 - 111
10X-RAY DIFFRACTION10chain 'B' and (resid 112 through 130 )B112 - 130
11X-RAY DIFFRACTION11chain 'B' and (resid 131 through 157 )B131 - 157
12X-RAY DIFFRACTION12chain 'B' and (resid 158 through 167 )B158 - 167

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