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- PDB-7snr: 2.00A Resolution Structure of NanoLuc Luciferase -

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Basic information

Entry
Database: PDB / ID: 7snr
Title2.00A Resolution Structure of NanoLuc Luciferase
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsOXIDOREDUCTASE / OPLOPHORUS BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE / NLUC / COELENTERAZINE / FURIMAZINE / BETA-BARREL / Selenomethionine
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / Calycin / extracellular region / ACETATE ION / CITRATE ANION / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / 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: 2.00A Resolution Structure of NanoLuc Luciferase
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)39,4475
Polymers39,1402
Non-polymers3073
Water2,720151
1
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8774
Polymers19,5701
Non-polymers3073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)19,5701
Polymers19,5701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.188, 55.800, 55.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

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


Mass: 19569.850 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.68 % / Mosaicity: 0.1 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.0 M ammonium citrate dibasic, 0.1 M sodium acetate trihydrate

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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: Jun 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.06 Å / Num. obs: 28770 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 26.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.046 / Rrim(I) all: 0.167 / Net I/σ(I): 14.3 / Num. measured all: 378302
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0513.51.3042782820620.7560.3671.3552.3100
8.94-44.0611.40.05444003870.9990.0160.0565098.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.1.29data scaling
SHELXphasing
PHENIXdev_4289refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→42.71 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 2742 5.08 %
Rwork0.1839 51253 -
obs0.1854 28770 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.87 Å2 / Biso mean: 34.7703 Å2 / Biso min: 12.76 Å2
Refinement stepCycle: final / Resolution: 2→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 21 151 2669
Biso mean--26.23 33.72 -
Num. residues----322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.030.29141390.252225092648
2.03-2.070.30291360.25625932729
2.07-2.110.3141200.233925692689
2.11-2.150.27431470.22725692716
2.15-2.20.25191270.210125472674
2.2-2.250.20561200.193525942714
2.25-2.310.25721380.201325682706
2.31-2.370.26221410.19525492690
2.37-2.440.24671390.197625622701
2.44-2.520.21641370.182125732710
2.52-2.610.23231020.194626022704
2.61-2.710.24171320.177825882720
2.71-2.840.28171330.188225622695
2.84-2.990.2381580.190225412699
2.99-3.170.22851350.180825512686
3.17-3.420.20261570.160725452702
3.42-3.760.18381210.168926032724
3.76-4.310.13971700.146725312701
4.31-5.420.1591700.144225112681
5.43-42.710.2481200.223825862706
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)
10.17780.07430.10690.0776-0.02650.08640.00410.0375-0.07210.0122-0.02250.0971-0.0203-0.0138-0.00020.1841-0.02090.03060.14-0.00440.1494124.64537.61437.427
20.07670.05120.00170.1074-0.06880.05980.14530.0070.179-0.1599-0.1004-0.0435-0.253-0.04450.00010.21680.02170.0380.1542-0.02020.1941131.18340.63738.534
30.27840.36460.2720.55270.2370.27170.01140.03360.07940.06020.0805-0.1326-0.06380.0260.00590.1735-0.00520.03340.1359-0.01430.2193133.64344.45336.675
40.10310.07640.03630.05140.02130.0344-0.02990.00060.1375-0.01750.03430.09790.0099-0.2192-00.1781-0.01240.02260.16040.01190.1618120.47638.38636.104
50.13420.0980.16520.11620.05540.39540.0467-0.15020.2334-0.1556-0.15860.0738-0.1091-0.6368-0.01170.3192-0.02350.0080.3867-0.02340.312108.95634.63615.262
60.2453-0.0911-0.19290.2785-0.04450.1764-0.024-0.62530.29590.0094-0.22140.20990.0846-0.5456-0.5224-0.07940.02110.08820.9127-0.28410.32295.47739.2613.514
70.00130.04320.04280.10210.20790.29820.04190.08240.070.0459-0.0934-0.0978-0.2208-0.2227-0.00060.23350.02580.00830.26540.02860.1778113.12538.58110.426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:26 )A2 - 26
2X-RAY DIFFRACTION2( CHAIN A AND RESID 27:52 )A27 - 52
3X-RAY DIFFRACTION3( CHAIN A AND RESID 53:132 )A53 - 132
4X-RAY DIFFRACTION4( CHAIN A AND RESID 133:168 )A133 - 168
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:52 )B1 - 52
6X-RAY DIFFRACTION6( CHAIN B AND RESID 53:100 )B53 - 100
7X-RAY DIFFRACTION7( CHAIN B AND RESID 101:168 )B101 - 168

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