PDB-8gy0: Agrocybe pediades linalool sunthase (Ap.LS)

ID or keywords:

Entry

Database: PDB / ID: 8gy0

Title

Agrocybe pediades linalool sunthase (Ap.LS)

Components

Terpene synthase

Keywords

BIOSYNTHETIC PROTEIN / Monoterpene synthase

Function / homology

Function and homology information

Lyases; Carbon-oxygen lyases; Acting on phosphates / isoprenoid biosynthetic process / lyase activity / metal ion binding
Similarity search - Function

Biological species

Agrocybe pediades (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.988 Å

Authors

Rehka, T. / Sharma, D. / Lin, F. / Lim, C. / Choong, Y.K. / Chacko, J. / Zhang, C.

Funding support

Singapore, 2items

Citation

Journal: Acs Catalysis / Year: 2023
Title: Structural Understanding of Fungal Terpene Synthases for the Formation of Linear or Cyclic Terpene Products.
Authors: T, R. / Sharma, D. / Lin, F. / Choong, Y.K. / Lim, C. / Jobichen, C. / Zhang, C.

History

Deposition	Sep 21, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	May 8, 2024	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gy0.cif.gz	141.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8gy0.ent.gz	107.3 KB	Display	PDB format
PDBx/mmJSON format	8gy0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gy0_validation.pdf.gz	441.4 KB	Display	wwPDB validaton report
Full document	8gy0_full_validation.pdf.gz	453.8 KB	Display
Data in XML	8gy0_validation.xml.gz	24 KB	Display
Data in CIF	8gy0_validation.cif.gz	32.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gy/8gy0 ftp://data.pdbj.org/pub/pdb/validation_reports/gy/8gy0	HTTPS FTP

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Related structure data

Related structure data	1ps1S 2wbuS 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	#201 - Sep 2016 Isoprene Synthase similarity (1)

Deposited unit

B: Terpene synthase

A: Terpene synthase

74.9 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)	69.925, 80.665, 69.906
Angle α, β, γ (deg.)	90.000, 96.050, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Terpene synthase Mass: 37439.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrocybe pediades (fungus) / Gene: D9613_012268 / Production host: Escherichia coli (E. coli) References: UniProt: A0A8H4VHP2, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.62 Å³/Da / Density % sol: 53.08 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 10mM MgCl2, 0.2 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5 and 18% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.98→50 Å / Num. obs: 48065 / % possible obs: 90.5 % / Redundancy: 5.8 % / R_sym value: 0.089 / Net I/σ(I): 29.7
Reflection shell	Resolution: 1.98→2.01 Å / Num. unique obs: 1368 / R_sym value: 0.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
MADSYS		phasing

Refinement

Method to determine structure:

MAD
Starting model: 1ps1, 2wbu

1ps1

2wbu

Resolution: 1.988→46.804 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.932 / SU B: 9.291 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.224 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2745	1831	4.158 %
R_work	0.2144	42208	-
all	0.217	-	-
obs	-	44039	82.681 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 66.281 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.179 Å²	-0 Å²	0.546 Å²
2-	-	-6.036 Å²	-0 Å²
3-	-	-	2.682 Å²

Refinement step

Cycle: LAST / Resolution: 1.988→46.804 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5049	0	0	80	5129

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	5179
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	4728
X-RAY DIFFRACTION	r_angle_refined_deg	1.448	1.642	7022
X-RAY DIFFRACTION	r_angle_other_deg	1.299	1.58	10863
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.734	5	626
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.4	22.381	294
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.269	15	846
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.85	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.068	0.2	672
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5922
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1282
X-RAY DIFFRACTION	r_nbd_refined	0.208	0.2	1259
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	4370
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	2593
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	2367
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.259	0.2	154
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.12	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.13	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.246	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.23	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	6.171	6.948	2510
X-RAY DIFFRACTION	r_mcbond_other	6.168	6.945	2509
X-RAY DIFFRACTION	r_mcangle_it	8.681	10.401	3134
X-RAY DIFFRACTION	r_mcangle_other	8.682	10.403	3135
X-RAY DIFFRACTION	r_scbond_it	6.093	7.284	2669
X-RAY DIFFRACTION	r_scbond_other	6.092	7.286	2670
X-RAY DIFFRACTION	r_scangle_it	8.904	10.741	3888
X-RAY DIFFRACTION	r_scangle_other	8.903	10.742	3889
X-RAY DIFFRACTION	r_lrange_it	11.68	80.467	6108
X-RAY DIFFRACTION	r_lrange_other	11.69	80.469	6096

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 (%)
1.988-2.039	0.341	70	0.393	1435	X-RAY DIFFRACTION	38.3635
2.039-2.095	0.425	80	0.354	1850	X-RAY DIFFRACTION	50.3391
2.095-2.156	0.379	85	0.328	2160	X-RAY DIFFRACTION	60.9723
2.156-2.222	0.332	113	0.343	2496	X-RAY DIFFRACTION	71.9526
2.222-2.295	0.333	105	0.324	2699	X-RAY DIFFRACTION	80.3899
2.295-2.375	0.363	131	0.295	2810	X-RAY DIFFRACTION	85.8686
2.375-2.465	0.356	121	0.271	2782	X-RAY DIFFRACTION	89.7928
2.465-2.566	0.368	114	0.264	2676	X-RAY DIFFRACTION	89.0805
2.566-2.679	0.294	117	0.236	2786	X-RAY DIFFRACTION	94.9313
2.679-2.81	0.323	115	0.215	2667	X-RAY DIFFRACTION	96.1964
2.81-2.962	0.29	113	0.237	2528	X-RAY DIFFRACTION	97.167
2.962-3.141	0.293	106	0.218	2483	X-RAY DIFFRACTION	98.4785
3.141-3.357	0.268	100	0.223	2315	X-RAY DIFFRACTION	98.4509
3.357-3.626	0.275	91	0.21	2126	X-RAY DIFFRACTION	97.9673
3.626-3.971	0.226	87	0.175	1954	X-RAY DIFFRACTION	97.2831
3.971-4.438	0.258	81	0.17	1824	X-RAY DIFFRACTION	99.374
4.438-5.121	0.243	68	0.177	1583	X-RAY DIFFRACTION	97.9241
5.121-6.263	0.262	60	0.219	1379	X-RAY DIFFRACTION	99.3099
6.263-8.821	0.242	46	0.173	1048	X-RAY DIFFRACTION	97.8533
8.821-46.804	0.229	28	0.2	607	X-RAY DIFFRACTION	99.374

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