PDB-7snw: 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhib...

ID or keywords:

Entry

Database: PDB / ID: 7snw

Title

1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576

Components

Oplophorus-luciferin 2-monooxygenase catalytic subunit

Keywords

OXIDOREDUCTASE/INHIBITOR / OPLOPHORUS BIOLUMINESCENT PROTEIN / NANOLUC LUCIFERASE / NLUC / COELENTERAZINE / FURIMAZINE / BETA-BARREL / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex

Function / homology

Function and homology information

Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / extracellular region
Similarity search - Function

Biological species

Oplophorus gracilirostris (crustacean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.8 Å

Authors

Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Encell, L.P. / Wood, K.V.

Funding support

United States, 1items

Citation

Journal: To be published
Title: 1.80A Resolution Structure of NanoLuc Luciferase with Bound Inhibitor PC 16026576
Authors: Encell, L.P. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Wood, M.G. / Wood, K.V.

History

Deposition	Oct 28, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7snw.cif.gz	234.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7snw.ent.gz	187.7 KB	Display	PDB format
PDBx/mmJSON format	7snw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sn/7snw ftp://data.pdbj.org/pub/pdb/validation_reports/sn/7snw	HTTPS FTP

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Related structure data

Related structure data	5iboS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#193 - Jan 2016 Siderocalin similarity (1) #78 - Jun 2006 Luciferase similarity (1)

Deposited unit

A: Oplophorus-luciferin 2-monooxygenase catalytic subunit

B: Oplophorus-luciferin 2-monooxygenase catalytic subunit

C: Oplophorus-luciferin 2-monooxygenase catalytic subunit

hetero molecules

60.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Oplophorus-luciferin 2-monooxygenase catalytic subunit

hetero molecules

defined by author
Evidence: gel filtration
20.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Oplophorus-luciferin 2-monooxygenase catalytic subunit

hetero molecules

defined by author
20.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Oplophorus-luciferin 2-monooxygenase catalytic subunit

hetero molecules

defined by author
20 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.561, 110.661, 161.141
Angle α, β, γ (deg.)	90.000, 99.380, 90.000
Int Tables number	5
Space group name H-M	I121

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Protein , 1 types, 3 molecules ABC

#1: Protein	Oplophorus-luciferin 2-monooxygenase catalytic subunit / 19kOLase Mass: 19429.164 Da / Num. of mol.: 3 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

#1: Protein

Oplophorus-luciferin 2-monooxygenase catalytic subunit / 19kOLase

Mass: 19429.164 Da / Num. of mol.: 3
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

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Non-polymers , 7 types, 524 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-9YR / 2-(methoxycarbonyl)thiophene-3-sulfonic acid Mass: 222.239 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₆O₅S₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-9Y4 / N-[(4-methylphenyl)methyl]-N~2~-phenylglycinamide Mass: 254.327 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₁₈N₂O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.57 Å³/Da / Density % sol: 73.09 % / Mosaicity: 0.15 °
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.8 M Magnesium Sulfate, 0.1 M Bis-Tris Propane

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-ID / Wavelength: 1 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.8→45.41 Å / Num. obs: 96289 / % possible obs: 99.5 % / Redundancy: 3.4 % / B_iso Wilson estimate: 26.01 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.046 / Net I/σ(I): 15.9 / Num. measured all: 324618 / Scaling rejects: 16

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	Net I/σ(I) obs	% possible all
1.8-1.83	3.3	0.734	15926	4769	0.62	1.7	99.9
9.86-45.41	3.4	0.024	1964	581	0.999	51.5	93.2

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.3 Å	28.38 Å
Translation	2.3 Å	28.38 Å

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.3.8	data scaling
PHASER	2.5.6	phasing
PHENIX	dev_4289	refinement
PDB_EXTRACT	3.27	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IBO

5ibo

Resolution: 1.8→35.93 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 17.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1751	4852	5.04 %
R_work	0.1582	91423	-
obs	0.1591	96275	99.46 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 97.14 Å² / B_iso mean: 30.968 Å² / B_iso min: 16.89 Å²

Refinement step

Cycle: final / Resolution: 1.8→35.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3991	0	184	504	4679
B_iso mean	-	-	41.48	38.56	-
Num. residues	-	-	-	-	510

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.82	0.3078	148	0.2964	3018	3166	100
1.82-1.84	0.3022	144	0.273	3074	3218	100
1.84-1.86	0.2988	156	0.2616	3034	3190	100
1.86-1.89	0.2656	175	0.2327	3086	3261	100
1.89-1.91	0.2518	158	0.2063	3032	3190	100
1.91-1.94	0.1996	150	0.1834	3056	3206	100
1.94-1.97	0.1866	152	0.1765	3066	3218	100
1.97-2	0.2088	155	0.1658	3046	3201	100
2-2.03	0.1864	167	0.1755	3037	3204	100
2.03-2.06	0.1966	167	0.1719	3058	3225	100
2.06-2.1	0.1954	172	0.1693	3063	3235	100
2.1-2.13	0.2017	181	0.1658	3038	3219	100
2.13-2.18	0.1685	166	0.1593	3042	3208	100
2.18-2.22	0.1706	184	0.1468	3059	3243	100
2.22-2.27	0.1902	169	0.1413	3001	3170	100
2.27-2.32	0.1639	151	0.1443	3087	3238	100
2.32-2.38	0.1666	182	0.1417	3028	3210	100
2.38-2.44	0.1802	163	0.1454	3046	3209	100
2.44-2.51	0.1612	145	0.1473	3100	3245	100
2.51-2.6	0.1768	151	0.1558	3055	3206	100
2.6-2.69	0.1966	161	0.1591	3054	3215	100
2.69-2.8	0.2071	149	0.165	3072	3221	100
2.8-2.92	0.1833	148	0.1657	3030	3178	99
2.92-3.08	0.1832	159	0.1689	3076	3235	99
3.08-3.27	0.1884	179	0.1678	3002	3181	99
3.27-3.52	0.1794	175	0.1575	3032	3207	99
3.52-3.88	0.1662	156	0.1402	3011	3167	98
3.88-4.44	0.1182	150	0.1253	3047	3197	98
4.44-5.59	0.1344	142	0.1252	3064	3206	98
5.59-35.93	0.163	197	0.1819	3009	3206	97

Refinement TLS params.

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

ID	L11 (°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)
1	4.3114	1.0782	0.1969	1.887	0.5705	2.8513	-0.0528	0.3469	0.1999	-0.2883	0.1493	-0.2118	-0.1872	0.3329	-0.0757	0.3212	-0.0362	-0.0055	0.3033	0.0247	0.1465	72.6288	113.5766	1.7946
2	0.9392	-1.9987	-1.1955	5.238	1.5637	3.4182	-0.0555	0.0622	-0.1512	0.466	-0.1483	0.4538	0.3054	-0.2332	0.1845	0.2537	-0.0302	0.0096	0.2353	-0.0121	0.2031	58.2335	105.7871	17.1028
3	6.6002	-1.31	-2.8455	1.7303	0.6315	2.9873	0.0206	-0.1014	0.0944	-0.2223	0.015	-0.2197	-0.09	0.3667	-0.018	0.272	-0.0395	-0.0063	0.3162	-0.0403	0.2063	74.1284	115.1988	12.2589
4	4.0423	1.1321	-1.0087	2.1806	0.1357	2.4668	-0.0552	-0.2202	0.2999	0.1849	0.0751	0.1851	0.004	0.1033	-0.0088	0.2761	0.002	-0.0127	0.222	-0.0785	0.1972	63.5624	118.652	27.2361
5	5.3595	-3.7288	-2.8476	5.3958	2.3906	3.2857	-0.0872	-0.1495	0.1396	0.0895	0.0565	-0.2147	-0.0393	0.4439	0.0422	0.2135	-0.0165	-0.0136	0.2676	-0.0345	0.1565	72.9613	114.0744	17.7246
6	2.8934	0.4629	-1.9477	2.3804	-0.1323	5.5092	0.1537	-0.1792	-0.0597	-0.0183	-0.0988	-0.3608	0.0686	0.6946	-0.0047	0.2122	0.0425	-0.0265	0.2936	-0.0135	0.2207	77.4581	101.2104	14.8916
7	1.2807	0.0577	0.0502	1.8539	-1.358	2.2009	-0.0194	0.1623	-0.0918	-0.2937	0.0443	-0.0594	0.2336	0.255	-0.0281	0.2777	-0.0018	0.0101	0.2348	-0.0244	0.1639	69.5694	102.5554	6.4321
8	5.7495	4.1149	0.1113	3.0006	0.2891	2.1791	-0.3816	0.3673	0.3986	-0.7686	0.3266	-0.0021	-0.2194	0.0988	0.037	0.3445	-0.0319	-0.0157	0.2811	0.026	0.1931	65.5201	112.9514	3.9543
9	2.8927	-1.1273	1.7605	1.8433	-1.0826	3.8712	0.0363	-0.2051	-0.4419	0.2192	0.0832	0.1788	0.3249	-0.0285	-0.0703	0.2272	0.0044	-0.0184	0.1856	0.0776	0.3699	53.7396	71.3361	43.5554
10	1.2524	1.2129	-1.1625	2.2532	0.0603	2.767	0.127	0.1702	0.2751	-0.0398	0.1875	0.3881	-0.2208	-0.2439	-0.3042	0.235	0.0648	-0.0157	0.2357	0.0756	0.3568	47.9923	92.0301	36.2784
11	2.8805	-1.6822	3.3419	4.1962	-2.7737	6.7202	0.0109	-0.2501	-0.3227	0.4434	0.1341	-0.0552	-0.086	0.1456	-0.1815	0.2034	0.0342	-0.0174	0.2817	0.0958	0.3617	60.967	76.5496	45.2007
12	1.5604	0.2273	-1.2927	1.439	-0.449	3.6358	0.1324	-0.1267	0.0126	0.0484	-0.0488	-0.1104	-0.1913	0.2198	-0.0757	0.1645	-0.0009	-0.0287	0.1827	0.0595	0.2174	62.442	87.9157	38.4791
13	2.1058	0.1336	-0.0639	5.2484	-0.436	1.2559	0.0351	-0.2885	-0.052	0.3235	-0.0256	0.0684	-0.0066	-0.0716	0.0005	0.249	0.0055	-0.0116	0.2559	0.0742	0.2422	53.1502	84.9153	51.8892
14	1.0734	1.1499	-0.2037	2.0957	0.04	1.8895	0.016	-0.0645	-0.1572	0.0825	-0.001	0.0498	0.091	-0.0806	-0.015	0.1722	0.0225	-0.0131	0.2094	0.0631	0.2991	48.5366	80.2435	43.8323
15	2.846	1.5268	1.4519	3.3046	1.0986	4.3545	0.0378	-0.406	0.2933	0.3619	-0.0961	0.2389	-0.1446	-0.1497	0.0667	0.1657	0.044	0.0431	0.2965	-0.0975	0.2624	42.5034	132.6145	53.2451
16	7.0858	-3.6082	-3.8273	5.8819	0.0267	3.0283	0.0367	0.4784	-0.1272	-0.3681	-0.2024	0.63	0.2773	-0.3831	0.146	0.2217	-0.0263	-0.0375	0.2377	-0.072	0.2174	46.334	121.826	33.6564
17	2.3392	-0.3052	-0.4041	3.1893	1.4635	2.7975	-0.1261	-0.2008	-0.0186	0.1123	0.0233	0.0597	0.0774	0.1333	0.1058	0.2009	0.0107	0.01	0.2128	-0.0135	0.184	48.5827	122.2411	48.1335
18	1.8784	-0.3904	-0.1939	4.4348	1.2887	2.5279	-0.0646	-0.284	-0.3434	0.1868	0.0335	-0.1321	0.4335	0.0476	0.0179	0.2411	0.0259	0.0021	0.1989	0.0358	0.2362	51.5817	111.3946	49.0728
19	1.1724	-0.2479	-0.3602	2.1324	-0.1275	0.9965	0.0211	-0.2147	0.1031	0.0597	0.087	-0.0738	0.0954	0.2411	-0.1085	0.1707	0.0082	-0.0199	0.2495	-0.0646	0.1966	57.1767	125.8344	47.2061
20	4.3612	-2.9413	-4.1973	6.0632	4.4775	6.4303	0.2059	-0.0651	0.4186	-0.2755	-0.1237	-0.0581	-0.3978	0.0059	-0.0816	0.1887	-0.0185	-0.0292	0.2256	-0.0855	0.2848	53.1844	137.4567	44.3414
21	2.5495	-0.5475	-1.7959	1.3199	0.8843	2.754	-0.0921	-0.1077	0.2116	-0.0064	0.06	0.1381	0.0257	0.0287	0.0176	0.175	-0.0008	-0.0129	0.2001	-0.0601	0.2259	46.867	131.6689	41.22
22	2.6025	-0.0795	-0.8038	2.7789	-1.3778	6.587	0.0679	-0.3824	0.0044	0.3383	0.0579	0.3666	-0.2318	0.1073	-0.1444	0.2012	-0.0155	0.012	0.2399	-0.0738	0.2713	39.9076	127.6914	48.0656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 16 )	A	-1 - 16
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 37 )	A	17 - 37
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 61 )	A	38 - 61
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 62 through 86 )	A	62 - 86
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 87 through 98 )	A	87 - 98
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 99 through 120 )	A	99 - 120
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 121 through 157 )	A	121 - 157
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 158 through 168 )	A	158 - 168
9	X-RAY DIFFRACTION	9	chain 'B' and (resid -1 through 16 )	B	-1 - 16
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 17 through 37 )	B	17 - 37
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 38 through 50 )	B	38 - 50
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 51 through 107 )	B	51 - 107
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 130 )	B	108 - 130
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 131 through 168 )	B	131 - 168
15	X-RAY DIFFRACTION	15	chain 'C' and (resid -1 through 16 )	C	-1 - 16
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 17 through 28 )	C	17 - 28
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 29 through 50 )	C	29 - 50
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 51 through 86 )	C	51 - 86
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 87 through 113 )	C	87 - 113
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 114 through 130 )	C	114 - 130
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 131 through 157 )	C	131 - 157
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 158 through 168 )	C	158 - 168

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 7 types, 524 molecules

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Movie

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 7 types, 524 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Phasing

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Processing

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Yorodumi