PDB-5jo7: Henbane premnaspirodiene synthase (HPS), also known as Henbane ve...

ID or keywords:

Entry

Database: PDB / ID: 5jo7

Title

Henbane premnaspirodiene synthase (HPS), also known as Henbane vetispiradiene synthase (HVS) from Hyoscyamus muticus

Components

Vetispiradiene synthase 1

Keywords

LYASE / terpene synthase / HPS / Hyoscyamus

Function / homology

Function and homology information

vetispiradiene synthase / vetispiradiene synthase activity / diterpenoid biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function

Biological species

Hyoscyamus muticus (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.15 Å

Authors

Koo, H.J. / Xu, Y. / Louie, G.V. / Bowman, M. / Noel, J.P.

Citation

Journal: To Be Published
Title: Functional study of terpene synthase from 512 mutant library of henbane premnaspirodiene synthase reveals protein residue interactions
Authors: Koo, H.J. / Xu, Y. / Louie, G.V. / Bowman, M. / Noel, J.P.

History

Deposition	May 2, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5jo7.cif.gz	844.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5jo7.ent.gz	703.7 KB	Display	PDB format
PDBx/mmJSON format	5jo7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5jo7_validation.pdf.gz	456.1 KB	Display	wwPDB validaton report
Full document	5jo7_full_validation.pdf.gz	481.5 KB	Display
Data in XML	5jo7_validation.xml.gz	76.8 KB	Display
Data in CIF	5jo7_validation.cif.gz	109.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jo/5jo7 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/5jo7	HTTPS FTP

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Related structure data

Related structure data	5eauS 5ik0 5ik6 5ika 5ikh S: Starting model for refinement
Similar structure data	1a98-1 3g4d-1 3n0g-2 3g4f-1 6o9q-d 1hpu-2 4ho4-d 5wzr-2 1hxg-d 4fev-7 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#201 - Sep 2016 Isoprene Synthase similarity (9) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

A: Vetispiradiene synthase 1

B: Vetispiradiene synthase 1

C: Vetispiradiene synthase 1

D: Vetispiradiene synthase 1

250 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Vetispiradiene synthase 1

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

2

B: Vetispiradiene synthase 1

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

3

C: Vetispiradiene synthase 1

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

4

D: Vetispiradiene synthase 1

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

Unit cell

Length a, b, c (Å)	100.449, 100.690, 222.730
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Vetispiradiene synthase 1 / HVS1 Mass: 62517.703 Da / Num. of mol.: 4 / Fragment: UNP residues 23-555 Source method: isolated from a genetically manipulated source Details: HPS with 22 amino acids truncated at N-terminus. GS at N-terminus is from cleaved thrombin site. Source: (gene. exp.) Hyoscyamus muticus (plant) / Plasmid: pH9GW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q39978, vetispiradiene synthase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Vetispiradiene synthase 1 / HVS1

Mass: 62517.703 Da / Num. of mol.: 4 / Fragment: UNP residues 23-555
Source method: isolated from a genetically manipulated source
Details: HPS with 22 amino acids truncated at N-terminus. GS at N-terminus is from cleaved thrombin site.
Source: (gene. exp.)

Hyoscyamus muticus (plant) / Plasmid: pH9GW / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q39978, vetispiradiene synthase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 887 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.38 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Hanging drop of 1ul of 20 mg/ml protein and 1 ul of 100 mM PIPES pH 6.5, 200 mM di-sodium tartrate and 23% PEG 20000 with 500 ul of 0.55 M NaCl in the bottom

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2014 / Details: mirrors
Radiation	Monochromator: double crystal si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.15→74.69 Å / Num. obs: 104879 / % possible obs: 85.07 % / Redundancy: 6.6 % / CC_1/2: 0.984 / R_merge(I) obs: 0.09316 / Net I/σ(I): 13.04
Reflection shell	Resolution: 2.15→2.227 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.4166 / Mean I/σ(I) obs: 2.15 / % possible all: 59.95

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
iMOSFLM		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EAU

5eau

Resolution: 2.15→74.688 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.9

	R_factor	Num. reflection	% reflection
R_free	0.2499	2191	2.09 %
R_work	0.1907	-	-
obs	0.192	104810	85.01 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.15→74.688 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16543	0	0	887	17430

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	16965
X-RAY DIFFRACTION	f_angle_d	1.127	22988
X-RAY DIFFRACTION	f_dihedral_angle_d	13.818	6301
X-RAY DIFFRACTION	f_chiral_restr	0.049	2572
X-RAY DIFFRACTION	f_plane_restr	0.006	2898

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.15-2.1968	0.2662	72	0.2157	3706	X-RAY DIFFRACTION	50
2.1968-2.2479	0.3271	122	0.2453	5680	X-RAY DIFFRACTION	76
2.2479-2.3041	0.3134	125	0.2474	5709	X-RAY DIFFRACTION	77
2.3041-2.3664	0.2848	126	0.1937	6131	X-RAY DIFFRACTION	82
2.3664-2.436	0.2575	137	0.1943	6151	X-RAY DIFFRACTION	83
2.436-2.5147	0.2866	132	0.1956	6213	X-RAY DIFFRACTION	83
2.5147-2.6046	0.2669	132	0.2169	6175	X-RAY DIFFRACTION	83
2.6046-2.7088	0.2815	132	0.2132	6228	X-RAY DIFFRACTION	83
2.7088-2.8321	0.2857	132	0.2105	6196	X-RAY DIFFRACTION	83
2.8321-2.9815	0.2883	134	0.2134	6225	X-RAY DIFFRACTION	83
2.9815-3.1683	0.2377	139	0.2082	6590	X-RAY DIFFRACTION	87
3.1683-3.4129	0.2316	152	0.204	7087	X-RAY DIFFRACTION	94
3.4129-3.7563	0.2311	156	0.182	7421	X-RAY DIFFRACTION	98
3.7563-4.2998	0.2294	162	0.16	7555	X-RAY DIFFRACTION	99
4.2998-5.4171	0.2286	166	0.1608	7656	X-RAY DIFFRACTION	100
5.4171-74.7333	0.2267	172	0.1802	7896	X-RAY DIFFRACTION	99

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	2.0581	-0.0701	-0.262	1.7488	1.1898	4.4638	0.0029	-0.0562	-0.0347	-0.0676	-0.0574	0.2823	0.0263	-0.4634	0.0984	0.1714	0.0285	0.0453	0.1657	-0.0257	0.2105	-15.6626	-2.9026	-50.3028
2	1.159	0.0787	0.6491	1.4734	0.209	1.6372	-0.0268	0.0813	0.1824	-0.2982	0.051	0.0359	-0.3725	-0.0868	-0.031	0.2465	0.0422	0.0669	0.1393	0.0113	0.1636	-5.8518	5.1185	-57.899
3	1.7683	-0.888	0.031	1.2463	0.1339	0.7621	0.0457	-0.0597	0.1323	0.1361	0.0053	-0.3026	0.0561	0.1539	-0.0726	0.1448	-0.027	0.0245	0.1644	-0.0151	0.1894	19.5705	-11.1296	-39.8466
4	2.4191	-1.1018	0.1922	2.0283	-0.0329	3.4138	0.1671	0.5265	0.1115	-0.3105	-0.1807	-0.319	-0.1319	0.2978	-0.0736	0.1732	0.0178	0.0924	0.1992	0.004	0.1798	13.2644	-12.7322	-57.1632
5	1.2404	-0.0838	0.1008	2.6228	1.1916	1.9426	0.079	0.1448	0.2229	-0.1324	0.0148	-0.1849	-0.1872	0.1165	0.0049	0.1644	-0.017	0.0777	0.1781	0.0257	0.1741	4.5066	-3.0274	-46.9962
6	2.5471	0.2573	0.1452	1.896	-0.3427	2.7735	0.1569	0.1448	-0.0599	-0.069	-0.1036	-0.3054	-0.0022	0.2795	-0.0456	0.152	0.0304	0.0479	0.2671	0.0606	0.3531	64.4738	11.3401	-52.513
7	1.9834	1.3347	0.1116	1.9779	-0.1772	4.8649	0.0641	0.0818	-0.496	0.0065	-0.0358	-0.2012	0.5284	0.4043	-0.0486	0.1929	0.03	0.0076	0.2164	0.0284	0.358	55.8695	-0.0966	-50.7625
8	4.5082	-1.6597	0.0255	1.9719	-0.3194	0.4803	0.0175	-0.306	-0.184	0.1961	0.0319	0.2028	-0.0406	-0.0429	-0.054	0.1788	-0.0349	0.042	0.2599	0.0067	0.1739	32.5525	14.2441	-36.2477
9	4.0427	-0.8291	-0.0689	1.4994	-0.041	1.56	0.0799	-0.2165	0.6824	0.1574	-0.0772	-0.0335	-0.107	0.087	-0.0042	0.1811	-0.0295	0.0669	0.1472	-0.0188	0.3156	32.0959	26.7276	-41.5504
10	3.7236	-1.3968	2.1653	2.9354	-0.857	4.953	0.3178	0.8809	-0.2511	-0.6369	0.0322	0.2997	0.2303	-0.4452	-0.2343	0.2886	0.0686	-0.0021	0.6095	0.0582	0.2919	32.0334	19.8141	-61.4655
11	2.8084	-0.4725	-0.4587	1.961	-1.1274	2.5317	0.2177	0.409	-0.1081	-0.316	-0.2173	-0.172	0.1457	-0.0339	-0.0293	0.1454	0.0368	0.0464	0.2891	0.0112	0.2592	44.4788	14.0766	-51.7266
12	5.4916	-0.8371	3.3602	2.3628	0.1257	7.2924	-0.2688	-0.0954	0.4	0.2263	0.1723	0.0682	-0.5997	0.0886	0.1473	0.1993	-0.0506	-0.027	0.2841	-0.137	0.2833	27.1385	40.1308	15.4714
13	3.4646	-0.7487	0.0678	2.1667	0.251	1.8063	-0.0518	0.6721	0.3584	-0.422	0.0024	-0.1707	-0.2634	0.2945	0.0552	0.2846	-0.0679	-0.0053	0.4851	-0.0213	0.2486	25.8283	37.5793	-8.708
14	1.528	-0.9865	-0.9889	0.883	-0.0193	1.7007	0.0954	0.3234	0.094	0.0149	0.1694	-0.3973	-0.0315	0.753	-0.1248	0.2009	0.0094	0.0043	0.6156	-0.1568	0.2855	37.472	29.6623	4.1318
15	1.0379	0.4125	-0.2838	2.3585	-0.3036	1.1957	-0.0507	-0.1423	-0.4271	0.0219	0.1725	0.1005	0.297	-0.0963	-0.1147	0.2624	0.0287	-0.0764	0.3441	-0.0325	0.3476	16.0363	7.1715	15.5575
16	1.9933	0.7006	0.0395	3.6962	1.5686	4.0847	-0.1379	0.7277	-0.5882	-0.7432	0.1805	-0.1883	0.673	0.1685	-0.0073	0.5492	-0.0621	-0.015	0.5055	-0.1886	0.3789	17.9614	10.5606	-7.9658
17	4.2145	-0.1617	1.881	0.8768	-0.3875	2.207	0.1709	0.1126	-0.2437	-0.1269	0.1285	-0.2333	0.4261	0.4442	-0.1904	0.2466	0.0512	-0.0305	0.2966	-0.108	0.219	25.4563	20.0993	8.6204
18	2.3812	0.2125	0.001	2.5002	-0.4959	1.2408	-0.2418	0.1287	-0.9682	0.0526	0.0598	-0.096	0.6216	-0.1884	0.1614	0.7156	-0.106	0.2678	0.3886	0.0888	0.9854	40.5484	-42.5359	4.7621
19	1.7331	1.3692	0.3694	2.47	-0.2415	1.6802	-0.6473	0.5154	-0.8237	-0.343	0.1307	0.5534	0.6469	-0.6411	0.3788	0.5575	-0.204	0.1451	0.4923	-0.0909	0.7862	32.2736	-31.6977	-1.9557
20	3.3737	1.0278	-0.0533	3.6064	-0.0066	0.7036	-0.4136	-0.4955	-0.0308	0.3817	0.394	0.6583	0.0946	-0.2639	0.0632	0.5641	0.2196	0.1418	0.5151	0.123	0.305	37.7394	-13.0068	19.9159
21	2.0421	-0.4854	-1.0225	3.3052	0.787	2.1755	-0.3378	-0.5274	0.2265	0.4755	0.4681	-0.3782	0.034	0.2767	-0.0413	0.3285	0.1232	-0.0595	0.3706	-0.058	0.2138	55.0698	-3.9811	14.4487
22	4.8627	0.6422	-0.9836	2.5999	-0.2402	5.0426	-0.4567	0.943	0.0444	-0.9766	0.2654	0.1278	-0.0585	-0.5207	0.1274	0.5347	-0.1187	0	0.3886	-0.0141	0.2627	47.5704	-10.7881	-6.6908
23	5.4455	-0.2433	-0.5691	2.7805	0.4168	3.1773	-0.5559	-0.1747	-0.2606	0.1117	0.2952	0.244	-0.1137	-0.4076	0.1954	0.4576	0.0465	0.1119	0.22	0.0806	0.4135	39.3556	-21.1022	9.5135

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 37 through 151 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 152 through 229 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 230 through 409 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 410 through 501 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 502 through 555 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 38 through 189 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 190 through 229 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 230 through 339 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 340 through 437 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 438 through 479 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 480 through 555 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 39 through 100 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 101 through 189 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 190 through 229 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 230 through 437 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 438 through 501 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 502 through 555 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 45 through 151 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 152 through 229 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 230 through 311 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 312 through 437 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 438 through 501 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 502 through 555 )

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