PDB-5c05: Crystal Structure of Gamma-terpinene Synthase from Thymus vulgaris

ID or keywords:

Entry

Database: PDB / ID: 5c05

Title

Crystal Structure of Gamma-terpinene Synthase from Thymus vulgaris

Components

Putative gamma-terpinene synthase

Keywords

BIOSYNTHETIC PROTEIN / terpenoid synthesis / gamma-terpinene / plant / terpene / plant protein

Function / homology

Function and homology information

terpene synthase activity / magnesium ion binding
Similarity search - Function

Biological species

Thymus vulgaris (garden thyme)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Parthier, C.P. / Rudolph, K. / Muller, Y.A. / Mueller-Uri, F.

Funding support

Germany, 1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Expression, crystallization and structure elucidation of gamma-terpinene synthase from Thymus vulgaris.
Authors: Rudolph, K. / Parthier, C. / Egerer-Sieber, C. / Geiger, D. / Muller, Y.A. / Kreis, W. / Muller-Uri, F.

History

Deposition	Jun 12, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jan 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 20, 2016	Group: Database references
Revision 1.2	Mar 7, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Jan 10, 2024	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	5c05.cif.gz	455.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5c05.ent.gz	374.2 KB	Display	PDB format
PDBx/mmJSON format	5c05.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5c05_validation.pdf.gz	450.7 KB	Display	wwPDB validaton report
Full document	5c05_full_validation.pdf.gz	454.3 KB	Display
Data in XML	5c05_validation.xml.gz	45 KB	Display
Data in CIF	5c05_validation.cif.gz	69.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c0/5c05 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/5c05	HTTPS FTP

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Related structure data

Related structure data	2ongS S: Starting model for refinement
Similar structure data	1n24-d 1n1b-d 6onm-1 1n20-d 4gmc-d 2onh-d 5trj-d 4j0a-d 2ong-d 4jtw-d Search similar-shape structures by Omokage search (details) 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	#201 - Sep 2016 Isoprene Synthase similarity (7) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

A: Putative gamma-terpinene synthase

B: Putative gamma-terpinene synthase

hetero molecules

131 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	50.200, 79.610, 93.320
Angle α, β, γ (deg.)	94.790, 103.310, 105.560
Int Tables number	1
Space group name H-M	P1

#1: Protein	Putative gamma-terpinene synthase Mass: 65349.785 Da / Num. of mol.: 2 / Fragment: residues 56-596 / Mutation: G356D, A565T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thymus vulgaris (garden thyme) / Plasmid: pET300/NT-DEST / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M3Q1Q3*PLUS
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 942 / 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: 2.73 Å³/Da / Density % sol: 55.05 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 20 mM Tris, 0.2 M Ammonium tartrate dibasic, 20% w/v Polyethylene glycol 3350

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
ROTATING ANODE			RIGAKU MICROMAX-007 HF	1	1.5418
SYNCHROTRON	PETRA III, EMBL c/o DESY	P13 (MX1)		2	0.97731

Detector

Type	ID	Detector	Date
MAR scanner 345 mm plate	1	IMAGE PLATE	Sep 12, 2013
DECTRIS PILATUS 6M-F	2	PIXEL	Oct 1, 2013

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	SINGLE WAVELENGTH	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.5418	1
2	0.97731	1

Reflection

Highest resolution: 1.65 Å / Num. obs: 154186 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 22.93 Å² / R_merge F obs: 0.997 / R_merge(I) obs: 0.103 / R_rim(I) all: 0.115 / Χ²: 0.986 / Net I/σ(I): 9.19 / Num. measured all: 745728

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.65-1.75		0.762	0.651	1.96	88882	26113	23289	0.757	89.2
1.75-1.9		0.9	0.373	3.3	101055	29548	26396	0.434	89.3
1.9-2.02		0.929	0.411	5.07	91544	17693	17340	0.457	98
2.02-2.25		0.971	0.235	7.88	126440	24230	23951	0.262	98.8
2.25-2.6		0.988	0.155	11.44	120809	22374	22215	0.172	99.3
2.6-3.19		0.992	0.106	15.25	100652	18923	18811	0.118	99.4
3.19-4.7		0.995	0.075	20.53	79823	15311	15234	0.083	99.5
4.7-10		0.996	0.06	22.2	33165	6271	6247	0.066	99.6
	10	0.997	0.046	21.3	3358	715	703	0.051	98.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XSCALE		data scaling
PHASER		phasing
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
Coot	0.82pre	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ONG

2ong

Resolution: 1.65→29.84 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 20.5 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1863	1990	1.29 %
R_work	0.1636	152073	-
obs	0.1639	154063	95.64 %

Solvent computation

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

Displacement parameters

B_iso max: 115.83 Å² / B_iso mean: 33.2757 Å² / B_iso min: 13.22 Å²

Refinement step

Cycle: final / Resolution: 1.65→29.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8579	0	32	942	9553
B_iso mean	-	-	40.29	41.72	-
Num. residues	-	-	-	-	1036

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	8903
X-RAY DIFFRACTION	f_angle_d	1.08	12067
X-RAY DIFFRACTION	f_chiral_restr	0.065	1313
X-RAY DIFFRACTION	f_plane_restr	0.007	1540
X-RAY DIFFRACTION	f_dihedral_angle_d	12.112	5258

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6499-1.6912	0.245	126	0.2534	10298	10424	90
1.6912-1.7369	0.2726	131	0.2311	10045	10176	89
1.7369-1.788	0.2289	125	0.2146	9437	9562	83
1.788-1.8457	0.2301	130	0.2079	10496	10626	93
1.8457-1.9117	0.2223	139	0.1921	10518	10657	93
1.9117-1.9882	0.1941	139	0.186	11239	11378	99
1.9882-2.0787	0.2209	160	0.1787	11164	11324	99
2.0787-2.1882	0.1974	147	0.1647	11215	11362	99
2.1882-2.3253	0.1916	148	0.1583	11253	11401	99
2.3253-2.5047	0.1864	138	0.1671	11337	11475	99
2.5047-2.7566	0.1951	150	0.1685	11241	11391	99
2.7566-3.1551	0.2133	154	0.1687	11304	11458	100
3.1551-3.9737	0.1789	150	0.1536	11293	11443	100
3.9737-29.8448	0.1396	153	0.1351	11233	11386	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	1.4448	-1.1293	1.3051	2.2926	-1.8302	3.4532	-0.1048	-0.026	0.3975	0.2565	-0.2758	-0.2994	-0.6952	0.3071	0.2655	0.3288	-0.0245	0.0104	0.2669	-0.0727	0.1975	15.7766	24.3148	82.2055
2	0.758	-0.1263	0.3448	2.0216	-0.2764	0.7488	0.0899	-0.1301	-0.2	0.1351	-0.1231	-0.2174	0.2215	0.3358	0.0273	0.2832	0.033	-0.0194	0.3436	0.0354	0.1888	20.529	1.9273	91.9889
3	2.1079	0.4427	-0.1273	1.8596	-0.2745	1.9264	0.1113	-0.306	-0.3938	0.2491	-0.0806	0.0607	0.5807	-0.1625	-0.0256	0.5078	-0.0402	-0.0369	0.3362	0.1239	0.2842	10.115	-13.2486	93.4123
4	1.709	-0.2316	-0.684	1.6113	0.7564	2.6753	0.0074	-0.3356	-0.2319	0.2662	-0.0275	0.2718	0.4272	-0.2496	0.002	0.4012	-0.1121	0.0212	0.3484	0.0806	0.2521	-0.5742	-8.2954	90.6065
5	0.5393	0.0006	0.3365	0.2846	-0.0666	1.5091	0.0376	-0.2499	0.0276	0.2099	-0.0579	0.0211	-0.1303	-0.1077	-0.0004	0.2375	-0.0039	0.0317	0.2712	-0.0271	0.1844	6.0516	14.1361	84.9953
6	0.7093	-0.2579	0.5303	1.0609	-0.9327	3.2058	-0.0238	-0.184	0.0601	0.1361	0.0278	0.1288	-0.186	-0.3839	-0.0169	0.162	0.0139	0.0272	0.1925	-0.024	0.183	2.855	17.1231	65.5004
7	1.035	0.0641	0.137	0.3028	-0.3674	0.73	-0.0614	0.0345	-0.0677	-0.0365	0.0509	0.0494	-0.0577	-0.0854	-0.008	0.1398	0.0212	0.0237	0.1514	-0.0234	0.188	0.5585	10.4214	50.7928
8	0.7546	0.4471	-0.003	0.9301	-0.0121	0.4877	0.0336	-0.0581	-0.1815	0.0392	-0.021	-0.0263	0.0682	0.0518	-0.0147	0.1725	0.0252	0.014	0.1819	0.0005	0.2061	6.5208	3.7319	55.1922
9	2.1078	0.9612	0.3363	1.6082	0.3306	1.6478	0.1139	-0.2349	-0.0692	0.1752	-0.1712	0.2336	0.2697	-0.3837	0.0594	0.2551	-0.0683	0.0242	0.2572	-0.0125	0.2469	-6.2716	-6.239	71.2285
10	0.729	0.7245	0.1644	2.3386	0.3702	1.6795	0.0094	-0.1561	0.0282	0.1601	-0.0454	0.2501	-0.0632	-0.1007	0.0305	0.2019	0.0116	0.0111	0.2016	-0.0048	0.152	4.7675	8.6073	75.6905
11	1.1179	-1.0409	0.7683	4.0432	-0.9947	1.39	-0.112	-0.1954	0.1651	0.6887	0.0482	0.2902	-0.172	-0.1163	0.0117	0.3192	-0.0183	0.0178	0.2495	-0.0655	0.3279	14.764	51.5071	56.193
12	0.7127	-0.2891	0.1369	1.1771	-0.1269	1.9256	-0.0623	0.2553	0.3551	-0.4148	0.0623	0.3999	-0.3323	-0.1843	-0.0169	0.3725	0.0006	-0.1226	0.2443	0.0752	0.407	10.4502	62.4449	29.5791
13	1.2175	-0.3158	0.2498	1.4205	-0.1879	1.3964	0.009	0.4146	0.351	-0.6894	-0.0014	0.0032	-0.3012	0.2176	-0.0559	0.6124	-0.0942	-0.0509	0.3321	0.1316	0.3089	21.7746	60.5913	18.2792
14	1.196	0.0357	-0.0966	1.884	0.2351	1.1348	-0.0702	0.1439	0.2898	-0.3223	0.0981	-0.1752	-0.2824	0.2678	0	0.2726	-0.0789	0.0043	0.2066	0.0454	0.2814	28.8042	59.5568	32.8646
15	0.4327	0.237	0.1752	2.194	-0.506	0.2404	-0.0181	-0.0283	0.1015	0.2008	-0.0117	-0.0924	-0.0757	0.0532	0.0176	0.1797	-0.0024	-0.011	0.1647	-0.0152	0.1708	21.3993	39.4857	50.2614
16	0.447	0.0806	0.3953	0.9962	-0.4401	0.5189	-0.0307	0.1479	-0.0486	-0.1489	-0.0127	-0.076	0.0232	0.1038	0.0557	0.1373	-0.0035	0.0229	0.1721	-0.0125	0.1391	22.6444	20.4915	37.0255
17	1.8331	0.3874	-0.7879	1.3037	-0.1964	1.5798	-0.0802	0.152	0.0765	-0.1658	0.0882	-0.077	0.0536	0.1985	0.0063	0.1993	-0.0087	-0.0246	0.2021	0.0053	0.1506	25.3769	33.31	28.2678
18	1.0427	0.1057	-0.7609	1.8252	0.2	1.7389	-0.0827	0.1185	0.109	-0.1385	0.1221	-0.0436	-0.0528	0.206	-0.0428	0.2519	-0.0347	-0.0215	0.2002	0.0176	0.2177	24.8952	43.5744	32.0383

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 65 through 99 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 100 through 138 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 139 through 190 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 191 through 228 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 229 through 302 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 303 through 331 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 332 through 380 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 381 through 479 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 480 through 545 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 546 through 596 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 65 through 99 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 100 through 162 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 163 through 208 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 209 through 270 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 271 through 331 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 332 through 449 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 450 through 521 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 522 through 596 )	B

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