PDB-8x9c: Class I terpene synthase: eudesmanediol synthase (apo-PeTS3)

ID or keywords:

Entry

Database: PDB / ID: 8x9c

Title

Class I terpene synthase: eudesmanediol synthase (apo-PeTS3)

Components

Terpenoid synthase

Keywords

LIGASE / sesquiterpene / terpene synthase

Function / homology

Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Terpenoid synthase

Function and homology information

Biological species

Penicillium expansum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.68 Å

Authors

Huang, Z.Y. / Li, W.L. / Xu, J.H.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Molecule insights of a dihydrated sesquiterpene synthase PeTS3
Authors: Huang, Z.Y. / Li, W.L. / Xu, J.H.

History

Deposition	Nov 29, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8x9c.cif.gz	138.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8x9c.ent.gz	106.6 KB	Display	PDB format
PDBx/mmJSON format	8x9c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8x9c_validation.pdf.gz	438.7 KB	Display	wwPDB validaton report
Full document	8x9c_full_validation.pdf.gz	444.6 KB	Display
Data in XML	8x9c_validation.xml.gz	30.8 KB	Display
Data in CIF	8x9c_validation.cif.gz	42.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x9/8x9c ftp://data.pdbj.org/pub/pdb/validation_reports/x9/8x9c	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&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 (1)

Deposited unit

A: Terpenoid synthase

B: Terpenoid synthase

75.4 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)	56.650, 118.960, 65.600
Angle α, β, γ (deg.)	90.00, 111.53, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Terpenoid synthase Mass: 37705.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium expansum (fungus) / Gene: PEX2_005160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A2JK86
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H₂O
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: 2.75 Å³/Da / Density % sol: 55.23 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 20% v/v ethylene glycol, 10% w/v PEG8000, 0.2% w/v cytidine, 0.2% w/v inosine, 0.2% w/v ribavirin, 0.2% w/v thymidine, 0.2% w/v uridine, 0.1 M imidazole-MES monohydrate Buffer pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 17, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979183 Å / Relative weight: 1
Reflection	Resolution: 1.68→61.02 Å / Num. obs: 91596 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.045 / Net I/σ(I): 18.3
Reflection shell	Resolution: 1.68→1.72 Å / Redundancy: 5.6 % / Num. unique obs: 6795 / CC_1/2: 0.731 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
xia2		data scaling
PDB_EXTRACT		data extraction
PHASER		phasing
xia2		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.68→33.25 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.209	4472	4.89 %
R_work	0.1912	-	-
obs	0.1921	91521	99.74 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.68→33.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4811	0	0	418	5229

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4934
X-RAY DIFFRACTION	f_angle_d	0.904	6672
X-RAY DIFFRACTION	f_dihedral_angle_d	4.545	658
X-RAY DIFFRACTION	f_chiral_restr	0.052	725
X-RAY DIFFRACTION	f_plane_restr	0.01	859

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 (%)
1.68-1.7	0.3369	141	0.3233	2867	X-RAY DIFFRACTION	100
1.7-1.72	0.3608	140	0.3123	2949	X-RAY DIFFRACTION	100
1.72-1.74	0.3429	147	0.2992	2849	X-RAY DIFFRACTION	100
1.74-1.76	0.3221	144	0.2778	2911	X-RAY DIFFRACTION	100
1.76-1.79	0.3002	159	0.2687	2894	X-RAY DIFFRACTION	100
1.79-1.81	0.2794	152	0.2457	2902	X-RAY DIFFRACTION	100
1.81-1.84	0.2902	169	0.2361	2894	X-RAY DIFFRACTION	100
1.84-1.86	0.249	165	0.233	2853	X-RAY DIFFRACTION	100
1.86-1.89	0.2717	153	0.2319	2888	X-RAY DIFFRACTION	100
1.89-1.92	0.258	138	0.2309	2914	X-RAY DIFFRACTION	100
1.92-1.96	0.2555	131	0.2387	2921	X-RAY DIFFRACTION	100
1.96-1.99	0.2498	152	0.218	2880	X-RAY DIFFRACTION	100
1.99-2.03	0.2969	142	0.2139	2951	X-RAY DIFFRACTION	100
2.03-2.07	0.226	150	0.2045	2847	X-RAY DIFFRACTION	100
2.07-2.12	0.2087	157	0.2068	2946	X-RAY DIFFRACTION	100
2.12-2.17	0.208	148	0.2011	2878	X-RAY DIFFRACTION	100
2.17-2.22	0.224	171	0.195	2853	X-RAY DIFFRACTION	100
2.22-2.28	0.2464	136	0.2048	2933	X-RAY DIFFRACTION	100
2.28-2.35	0.2225	155	0.2043	2917	X-RAY DIFFRACTION	100
2.35-2.42	0.2253	123	0.1951	2903	X-RAY DIFFRACTION	100
2.42-2.51	0.2226	146	0.1991	2911	X-RAY DIFFRACTION	100
2.51-2.61	0.2233	144	0.2033	2904	X-RAY DIFFRACTION	100
2.61-2.73	0.2234	144	0.2039	2928	X-RAY DIFFRACTION	100
2.73-2.87	0.2142	157	0.1961	2901	X-RAY DIFFRACTION	100
2.87-3.05	0.2125	185	0.2009	2854	X-RAY DIFFRACTION	100
3.05-3.29	0.1758	142	0.1949	2930	X-RAY DIFFRACTION	99
3.29-3.62	0.2069	133	0.1894	2921	X-RAY DIFFRACTION	100
3.62-4.14	0.1737	159	0.1648	2898	X-RAY DIFFRACTION	100
4.14-5.21	0.1878	132	0.1524	2954	X-RAY DIFFRACTION	100
5.21-33.25	0.172	157	0.1674	2898	X-RAY DIFFRACTION	98

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