PDB-9k9y: Crystal structure of bicyclogermacrene synthase with FsPP

ID or keywords:

Entry

Database: PDB / ID: 9k9y

Title

Crystal structure of bicyclogermacrene synthase with FsPP

Components

Bicyclogermacrene synthase

Keywords

LYASE / Terpene synthase / complex with FsPP and Mg

Function / homology

Function and homology information

bicyclogermacrene synthase / farnesyl diphosphate catabolic process / bicyclogermacrene biosynthetic process / sesquiterpene synthase activity / diterpenoid biosynthetic process / magnesium ion binding
Similarity search - Function

Biological species

Phyla dulcis (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.89 Å

Authors

Tian, B.X. / Fan, S.L. / Chen, X.L. / Guo, L.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Enhancing Enzyme Activity with Mutation Combinations Guided by Few-shot Learning and Causal Inference
Authors: Guo, L. / Yan, X.G. / Nie, S.X. / Ge, M.Y. / Li, Y.K. / Lu, Y.L. / Li, W.G. / Zhang, X.C. / Liang, D.M. / Zhao, Y.H. / Tang, H.X. / Chen, X.L. / Fan, S.L. / Tang, Y.F. / Qiao, J.J. / Tian, B.X.

History

Deposition	Oct 28, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	May 13, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9k9y.cif.gz	417.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9k9y.ent.gz	344.8 KB	Display	PDB format
PDBx/mmJSON format	9k9y.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/k9/9k9y ftp://data.pdbj.org/pub/pdb/validation_reports/k9/9k9y	HTTPS FTP

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Related structure data

Related structure data	9k9xC 9ka1C 3g4dS S: Starting model for refinement C: citing same article (ref.)
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	#201 - Sep 2016 Isoprene Synthase similarity (9) #96 - Dec 2007 Oxidosqualene Cyclase similarity (1)

Deposited unit

A: Bicyclogermacrene synthase

B: Bicyclogermacrene synthase

hetero molecules

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

1

A: Bicyclogermacrene synthase

hetero molecules

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

2

B: Bicyclogermacrene synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	57.410, 131.650, 83.160
Angle α, β, γ (deg.)	90.00, 93.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Bicyclogermacrene synthase / Terpene synthase 5 / LdTPS5 Mass: 66560.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phyla dulcis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: J7LMP2, bicyclogermacrene synthase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE Mass: 398.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₈O₆P₂S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.81 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 19% (w/v) polyethylene glycol 3350, 0.1 M HEPES pH 7.5, and 0.2 M MgCl2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 9, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.89→57.31 Å / Num. obs: 53213 / % possible obs: 99.5 % / Redundancy: 6.1 % / R_pim(I) all: 0.145 / Net I/σ(I): 10.4
Reflection shell	Resolution: 2.89→2.99 Å / R_merge(I) obs: 0.145 / Num. unique obs: 53213

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3G4D

3g4d

Resolution: 2.89→57.31 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2435	3851	7.24 %
R_work	0.2118	-	-
obs	0.2141	53213	97.79 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.89→57.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8152	0	50	0	8202

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_dihedral_angle_d	11.177	1109
X-RAY DIFFRACTION	f_chiral_restr	0.043	1205
X-RAY DIFFRACTION	f_plane_restr	0.007	1449

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 (%)
2.89-2.93	0.4357	124	0.3765	1713	X-RAY DIFFRACTION	97
2.93-2.96	0.3438	137	0.3674	1779	X-RAY DIFFRACTION	97
2.96-3	0.4102	156	0.3555	1776	X-RAY DIFFRACTION	98
3.04-3.09	0.3396	134	0.3341	1718	X-RAY DIFFRACTION	98
3.09-3.13	0.3078	130	0.2961	1826	X-RAY DIFFRACTION	99
3.13-3.18	0.3245	147	0.2815	1818	X-RAY DIFFRACTION	98
3.29-3.35	0.2886	133	0.2601	1785	X-RAY DIFFRACTION	98
3.35-3.41	0.2818	159	0.2605	1756	X-RAY DIFFRACTION	98
3.41-3.48	0.2666	100	0.2543	1766	X-RAY DIFFRACTION	98
3.48-3.56	0.2483	150	0.2389	1804	X-RAY DIFFRACTION	99
3.56-3.64	0.3069	142	0.2489	1770	X-RAY DIFFRACTION	98
3.64-3.73	0.2945	122	0.2406	1775	X-RAY DIFFRACTION	98
3.73-3.83	0.2491	144	0.2003	1788	X-RAY DIFFRACTION	99
3.83-3.95	0.2833	146	0.2126	1749	X-RAY DIFFRACTION	98
3.95-4.07	0.2537	125	0.1811	1797	X-RAY DIFFRACTION	98
4.07-4.22	0.2251	137	0.1925	1737	X-RAY DIFFRACTION	99
4.22-4.39	0.2007	146	0.1831	1798	X-RAY DIFFRACTION	98
4.39-4.59	0.209	140	0.1715	1725	X-RAY DIFFRACTION	98
4.59-4.83	0.1823	136	0.1666	1786	X-RAY DIFFRACTION	98
4.83-5.13	0.2502	143	0.1818	1779	X-RAY DIFFRACTION	98
5.13-5.53	0.2171	136	0.1975	1731	X-RAY DIFFRACTION	98
5.53-6.08	0.2557	144	0.2241	1772	X-RAY DIFFRACTION	98
6.08-6.96	0.2948	128	0.2203	1779	X-RAY DIFFRACTION	97
6.96-8.76	0.1665	135	0.165	1720	X-RAY DIFFRACTION	96

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	0.9459	0.2167	-0.3339	0.4629	-0.1293	0.9405	-0.0569	-0.1318	-0.2537	-0.1031	0.0537	0.1738	0.3512	0.0358	0.0002	0.6187	0.1075	-0.0549	0.4665	0.0441	0.4937	3.5705	-16.2023	16.8344
2	0.089	0.023	0.0538	0.0725	-0.0229	0.0502	0.006	0.0307	-0.0308	0.1052	-0.3578	-0.2917	0.0565	0.6487	0.0002	0.502	0.1482	-0.0178	0.9017	0.1071	0.5304	22.1867	-12.1999	21.399
3	0.0717	0.0864	0.0004	0.9861	0.2375	0.0746	-0.0688	0.442	-0.0972	-0.664	-0.1343	0.3508	0.2253	0.4802	-0.0236	0.5925	0.2072	0.0003	0.6259	0.0144	0.4193	13.0515	-13.3586	8.2937
4	0.3536	-0.2737	0.0441	0.3205	0.1075	0.3983	0.016	0.0397	0.0465	-0.1419	0.0679	-0.0979	0.0494	-0.0509	0	0.3714	0.0371	-0.0118	0.3602	0.0035	0.3995	-4.7331	11.6109	9.8643
5	0.1302	0.0451	0.112	0.0312	0.0234	0.0978	0.0924	-0.0736	-0.1389	-0.0448	-0.2268	-0.0013	-0.1441	-0.2145	-0.0007	0.3533	0.0063	-0.0454	0.44	0.0405	0.5359	-14.2956	17.3922	15.507
6	0.0386	-0.0664	0.0427	0.1086	-0.0759	0.0374	-0.2105	0.1166	0.0683	0.2681	0.211	0.0491	-0.0777	-0.0935	0.0004	0.4864	0.0164	-0.0295	0.4648	-0.0518	0.5376	-0.6057	18.2413	23.909
7	0.0331	-0.0428	0.0151	0.1197	-0.1498	0.2513	-0.0747	-0.0158	-0.0193	0.0118	0.0304	-0.0476	0.1834	-0.276	0.0099	0.6398	0.0761	0.0106	0.5554	-0.0347	0.5959	0.0282	5.5717	29.4059
8	0.3042	-0.389	0.0703	0.5443	-0.1939	0.193	0.0384	0.0236	-0.0442	0.0588	-0.1682	-0.0482	0.1175	0.2125	-0	0.4506	-0.0144	-0.0119	0.4781	0.0454	0.4166	7.2255	0.451	15.8094
9	0.4247	0.1928	-0.1476	0.1767	-0.2052	0.3801	0.1115	-0.3509	0.0641	0.0807	0.0742	-0.3021	-0.0104	0.2323	0.0001	0.4548	-0.0776	-0.0299	0.7117	-0.0694	0.5781	24.9057	-6.2537	-10.3762
10	0.1974	-0.1148	0.0095	0.1773	-0.1837	0.2519	-0.1247	0.1038	0.0499	0.0355	-0.1027	-0.1102	0.0557	0.2079	-0	0.4465	-0.0311	-0.0449	0.4565	-0.0352	0.3853	11.976	-21.6159	-31.5427
11	0.1464	0.0295	-0.0345	0.1913	0.1144	0.0949	0.1304	0.3398	-0.0293	-0.1549	-0.1629	0.4346	-0.3863	-0.6129	-0.0014	0.3158	0.038	-0.0304	0.6831	-0.0485	0.4579	-4.3795	-13.9667	-32.5111
12	1.1745	-0.0182	-0.4914	0.5732	0.0998	1.1651	0.3977	-0.3215	0.331	-0.1509	-0.0587	-0.0719	-0.232	-0.0313	0.4662	0.4551	-0.0607	0.1388	0.3165	-0.0966	0.5064	19.2227	4.5258	-17.6589
13	0.6045	-0.2991	0.8042	0.3274	-0.1725	1.3707	0.3884	-0.0832	0.4443	-0.094	-0.0421	-0.1178	-0.3945	0.6131	0.3435	0.8296	-0.1795	0.3888	0.5374	0.0075	1.0052	26.282	17.0923	-28.8455
14	0.0193	0.0407	0.0345	0.1468	0.1007	0.0693	0.2	0.4227	0.224	-0.2412	0.0755	-0.0669	-0.2995	-0.207	0.0097	0.8557	0.0341	0.2354	0.8862	0.1697	0.7305	19.8603	5.3397	-37.7489
15	0.5273	0.0963	-0.0713	0.2437	0.2307	0.2454	0.2585	-0.0438	0.2681	-0.0876	-0.1489	-0.0138	0.0108	0.0513	0.0003	0.4757	0.0759	0.0616	0.4264	0.0214	0.5043	11.965	0.3741	-24.1545

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 26 through 157 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 158 through 195 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 196 through 238 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 239 through 348 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 349 through 374 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 375 through 429 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 430 through 496 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 497 through 564 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 23 through 72 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 73 through 133 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 134 through 197 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 198 through 348 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 349 through 430 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 431 through 497 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 498 through 564 )

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