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- PDB-7sns: 1.55A Resolution Structure of NanoLuc Luciferase -

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Basic information

Entry
Database: PDB / ID: 7sns
Title1.55A Resolution Structure of NanoLuc Luciferase
ComponentsOplophorus-luciferin 2-monooxygenase catalytic subunit
KeywordsOXIDOREDUCTASE / OPLOPHORUS BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE / NLUC / COELENTERAZINE / FURIMAZINE / BETA-BARREL
Function / homologyOplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / Calycin / extracellular region / ACETATE ION / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Function and homology information
Biological speciesOplophorus gracilirostris (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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: 1.55A 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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,89824
Polymers77,7174
Non-polymers1,18120
Water12,448691
1
A: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7837
Polymers19,4291
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6655
Polymers19,4291
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7246
Polymers19,4291
Non-polymers2955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Oplophorus-luciferin 2-monooxygenase catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7246
Polymers19,4291
Non-polymers2955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.332, 61.266, 94.969
Angle α, β, γ (deg.)90.000, 92.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19429.164 Da / Num. of mol.: 4
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.: 20 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8 M Sodium acetate trihydrate, 0.1 M BIS-TRIS propane

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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: Aug 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→47.45 Å / Num. obs: 101022 / % possible obs: 98.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.9 / Num. measured all: 332167 / Scaling rejects: 213
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.55-1.583.20.5711635650400.7791.899.8
8.49-47.453.40.02722066480.99933.496.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å47.47 Å
Translation2.1 Å47.47 Å

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Processing

Software
NameVersionClassification
PHENIXdev_4289refinement
XDSdata reduction
Aimless0.5.15data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IBO

5ibo


Resolution: 1.55→39.04 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1894 5052 5 %
Rwork0.1639 95933 -
obs0.1651 100985 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.66 Å2 / Biso mean: 27.2413 Å2 / Biso min: 12.53 Å2
Refinement stepCycle: final / Resolution: 1.55→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 80 691 6054
Biso mean--27.53 36.71 -
Num. residues----685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.28141830.249332183401100
1.57-1.590.27011790.238231623341100
1.59-1.610.26991820.236732203402100
1.61-1.630.25411560.234131903346100
1.63-1.650.27441930.230531813374100
1.65-1.670.24951870.223532243411100
1.67-1.690.23611570.216832513408100
1.69-1.720.23851610.208631683329100
1.72-1.750.23761700.199832383408100
1.75-1.770.24321800.192731863366100
1.77-1.80.22331690.197232773446100
1.8-1.840.21321690.187131563325100
1.84-1.870.21341730.178732173390100
1.87-1.910.20811860.165432143400100
1.91-1.950.19291660.15593243340999
1.95-20.18311370.15831893326100
2-2.050.19271490.157632753424100
2.05-2.10.18021770.1573206338399
2.1-2.170.1791450.14873182332799
2.17-2.240.20192040.15143121332599
2.24-2.320.16091810.15523196337799
2.32-2.410.17611470.15723263341099
2.41-2.520.20861590.16133176333599
2.52-2.650.18621760.15723194337098
2.65-2.820.17611440.16253163330797
2.82-3.030.18741590.16413153331297
3.03-3.340.17791610.15563150331196
3.34-3.820.16921570.14793165332297
3.82-4.810.14081580.13093127328595
4.81-39.040.20851870.18373228341597
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)
10.4849-0.2201-0.49411.2054-0.04850.6986-0.0707-0.28630.0725-0.08-0.09960.1608-0.0553-0.33260.06910.13490.0163-0.01750.338-0.06720.152844.650731.034382.3655
21.3518-2.2189-2.30924.10244.29134.4637-0.05870.066-0.1711-0.67220.05710.0531-1.02210.4046-0.02980.2758-0.0532-0.00160.3258-0.06890.239663.562132.244779.159
32.7423-0.5505-2.84910.59840.46433.8770.0189-0.3403-0.18470.0117-0.16820.12160.0787-0.18070.10340.1392-0.03280.00250.3043-0.02480.163647.620922.233984.8339
42.18721.21050.65484.16661.18422.296-0.0299-0.3477-0.1385-0.03230.0896-0.6183-0.00770.2642-0.06590.24080.058-0.00850.25220.02240.260863.361117.69679.7029
50.7946-0.11750.02830.5618-0.07760.07170.0999-0.44670.15070.1024-0.16160.054-0.0652-0.33130.02480.1493-0.01170.00750.4543-0.08730.177949.114330.47992.8603
65.53992.11221.59411.8751.12662.1381-0.0201-0.32210.4438-0.2102-0.04960.0813-0.3976-0.36250.08580.1680.0773-0.00860.3317-0.10380.221643.76236.063482.9158
72.83462.26081.58195.02361.32131.46070.0892-0.23270.0216-0.3156-0.14710.08510.0825-0.26010.08230.21660.03920.00430.2614-0.03770.176543.931829.577477.9597
80.4816-0.2289-0.45061.2862-0.62812.208-0.04740.10560.056-0.11980.0210.1211-0.03490.08270.00870.1419-0.0117-0.00610.18450.03560.17237.81524.70281.9333
92.03850.13730.15881.1005-0.33080.60720.0047-0.4871-0.35340.01080.3850.6612-0.2752-0.7978-0.27850.22280.0581-0.00720.4140.0460.328426.511315.137181.0616
104.1132-3.52084.35792.9703-3.64955.78970.0807-0.4599-0.2146-0.06870.13780.14440.0377-0.5927-0.14970.19740.00420.01340.33580.03010.227133.156211.386887.251
111.5670.2470.86561.68840.02131.98860.1465-0.1709-0.12390.0343-0.08240.1290.1546-0.1068-0.05410.1092-0.0145-0.01110.18450.04660.174539.1378-0.334787.7313
127.8855-2.9177-2.26627.02591.59934.35970.22360.104-0.7482-0.1208-0.23790.37270.5220.0205-0.040.3153-0.00270.04210.1052-0.0370.219155.28438.109854.4022
131.4014-0.7875-0.51980.6047-0.05932.0382-0.0289-0.18180.1387-0.0282-0.0213-0.1173-0.06640.13660.03390.15990.00970.00930.0978-0.00250.150359.182626.563964.2898
144.7051-0.619-3.86492.63062.12187.65380.187-0.80240.30410.31020.00610.2958-0.45350.5109-0.18780.4061-0.05710.0560.3392-0.06330.368757.986938.302865.8387
151.7773-0.6925-0.32162.91921.20082.47810.01020.0258-0.015-0.4207-0.11550.0332-0.2929-0.19840.09520.21440.0018-0.00180.1386-0.00430.159149.166723.846258.1987
162.2388-0.2329-0.3531.32480.0751.50240.0637-0.09890.5038-0.24590.0329-0.0045-0.3715-0.1003-0.11540.23970.0174-0.03460.1236-0.00460.240648.328632.736557.0212
171.5141-0.67170.21991.07060.5731.2345-0.08650.0516-0.0074-0.13190.0333-0.12480.03980.15280.04450.2044-0.00570.03780.0753-0.00460.151761.323122.025156.3545
181.7110.28930.32980.58940.06951.41080.0494-0.06790.02370.0984-0.0533-0.0019-0.0729-0.0678-0.01290.16820.0328-0.00090.0959-0.01990.145528.690715.892760.6216
192.795-0.54414.27262.6834-2.96938.27590.3573-0.6749-0.164-0.2381-0.02850.23990.8609-0.8383-0.24520.2827-0.0741-0.06150.31950.00010.301728.2628-2.98263.4098
200.82720.03790.55981.5894-0.92831.71010.0202-0.05060.0393-0.07540.00530.0852-0.0775-0.0121-0.02950.18850.0072-0.0060.1186-0.00310.171537.782613.397757.7988
213.33110.75690.73882.11730.52022.8380.1830.0702-0.8168-0.19-0.1006-0.10780.41640.1951-0.07410.24310.0401-0.01560.2152-0.010.369142.6098-2.851362.4004
221.1487-0.7330.88380.8144-1.1391.66580.02240.0914-0.0588-0.1611-0.02480.0702-0.01910.1176-0.0440.27310.0017-0.04330.1298-0.01480.222434.735810.111550.2622
231.361-0.20080.31761.2390.17122.0901-0.0114-0.08260.0122-0.11510.01960.1507-0.0778-0.2020.00290.17750.0168-0.01580.11350.0020.180626.066314.551755.4435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )A-1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 34 )A25 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 61 )A35 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 86 )A62 - 86
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 143 )A87 - 143
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 157 )A144 - 157
7X-RAY DIFFRACTION7chain 'A' and (resid 158 through 169 )A158 - 169
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 50 )B-1 - 50
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 86 )B51 - 86
10X-RAY DIFFRACTION10chain 'B' and (resid 87 through 98 )B87 - 98
11X-RAY DIFFRACTION11chain 'B' and (resid 99 through 169 )B99 - 169
12X-RAY DIFFRACTION12chain 'C' and (resid -2 through 7 )C-2 - 7
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 24 )C8 - 24
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 34 )C25 - 34
15X-RAY DIFFRACTION15chain 'C' and (resid 35 through 61 )C35 - 61
16X-RAY DIFFRACTION16chain 'C' and (resid 62 through 111 )C62 - 111
17X-RAY DIFFRACTION17chain 'C' and (resid 112 through 169 )C112 - 169
18X-RAY DIFFRACTION18chain 'D' and (resid -1 through 24 )D-1 - 24
19X-RAY DIFFRACTION19chain 'D' and (resid 25 through 34 )D25 - 34
20X-RAY DIFFRACTION20chain 'D' and (resid 35 through 61 )D35 - 61
21X-RAY DIFFRACTION21chain 'D' and (resid 62 through 86 )D62 - 86
22X-RAY DIFFRACTION22chain 'D' and (resid 87 through 111 )D87 - 111
23X-RAY DIFFRACTION23chain 'D' and (resid 112 through 169 )D112 - 169

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