PDB-5nx5: Crystal structure of Linalool/Nerolidol synthase from Streptomyce...

ID or keywords:

Entry

Database: PDB / ID: 5nx5

Title

Crystal structure of Linalool/Nerolidol synthase from Streptomyces clavuligerus in complex with 2-fluorogeranyl diphosphate

Components

Pentalenene synthase

Keywords

LIGASE / terpene synthase / linalool / nerolidol / monoterpenoid

Function / homology

Function and homology information

R-linalool synthase / R-linalool synthase activity / geranyl diphosphate metabolic process / farnesyl diphosphate metabolic process / magnesium ion binding
Similarity search - Function

Biological species

Streptomyces clavuligerus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.82 Å

Authors

Karuppiah, V. / Leys, D. / Scrutton, N.S.

Funding support

United Kingdom, 1items

Citation

Journal: ACS Catal / Year: 2017
Title: Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.
Authors: Karuppiah, V. / Ranaghan, K.E. / Leferink, N.G.H. / Johannissen, L.O. / Shanmugam, M. / Ni Cheallaigh, A. / Bennett, N.J. / Kearsey, L.J. / Takano, E. / Gardiner, J.M. / van der Kamp, M.W. / ...

History

Deposition	May 9, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5nx5.cif.gz	251.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5nx5.ent.gz	201.7 KB	Display	PDB format
PDBx/mmJSON format	5nx5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5nx5_validation.pdf.gz	722.1 KB	Display	wwPDB validaton report
Full document	5nx5_full_validation.pdf.gz	724.2 KB	Display
Data in XML	5nx5_validation.xml.gz	27.5 KB	Display
Data in CIF	5nx5_validation.cif.gz	41.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/5nx5 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/5nx5	HTTPS FTP

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Related structure data

Related structure data	5nx4C 5nx6C 5nx7C 1ps1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5bsw-2 5nx4-d 3n5e-d 4fgt-1 1zpu-2 3kgb-1 5e75-d 1zpu-1 5bsm-2 6su6-2 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 (1)

Deposited unit

A: Pentalenene synthase

B: Pentalenene synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	139.370, 139.370, 86.060
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

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Protein , 1 types, 2 molecules AB

#1: Protein	Pentalenene synthase / Linalool/Nerolidol synthase Mass: 36450.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_p1185 / Production host: Escherichia coli (E. coli) / References: UniProt: D5SL78, pentalenene synthase

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Non-polymers , 6 types, 524 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-0FV / (2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate / 2-fluorogeranyl diphosphate Mass: 332.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₉FO₇P₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 514 / 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: 3.22 Å³/Da / Density % sol: 61.83 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.12 M Alcohols (0.2M 1,6-hexanediol, 0.2M 1-nutanol, 0.2M 1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol), 0.1 M Buffer System 2 (1.0M sodium HEPES, MOPS (acid)) ...Details: 0.12 M Alcohols (0.2M 1,6-hexanediol, 0.2M 1-nutanol, 0.2M 1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol), 0.1 M Buffer System 2 (1.0M sodium HEPES, MOPS (acid)) pH 7.5 and 50 % v/v precipitant Mix 3 (40% v/v glycerol, 20% w/v PEG 4000)

Crystal

Density Matthews: 3.22 Å³/Da / Density % sol: 61.83 %

Crystal grow

Temperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Alcohols (0.2M 1,6-hexanediol, 0.2M 1-nutanol, 0.2M 1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol), 0.1 M Buffer System 2 (1.0M sodium HEPES, MOPS (acid)) ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.99 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 1.82→36.62 Å / Num. obs: 73739 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.057 / R_pim(I) all: 0.024 / Net I/σ(I): 18.2
Reflection shell	Resolution: 1.82→1.85 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3654 / CC_1/2: 0.51 / R_pim(I) all: 0.563 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2621: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1

Resolution: 1.82→34.843 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.24

	R_factor	Num. reflection	% reflection
R_free	0.1889	3550	4.81 %
R_work	0.1667	-	-
obs	0.1678	73730	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.82→34.843 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4418	0	58	514	4990

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4615
X-RAY DIFFRACTION	f_angle_d	0.94	6263
X-RAY DIFFRACTION	f_dihedral_angle_d	9.916	2669
X-RAY DIFFRACTION	f_chiral_restr	0.049	665
X-RAY DIFFRACTION	f_plane_restr	0.007	816

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 (%)
1.82-1.845	0.3438	165	0.2914	2797	X-RAY DIFFRACTION	100
1.845-1.8713	0.3122	115	0.2689	2782	X-RAY DIFFRACTION	100
1.8713-1.8992	0.2787	128	0.2629	2786	X-RAY DIFFRACTION	100
1.8992-1.9289	0.2898	138	0.2416	2799	X-RAY DIFFRACTION	100
1.9289-1.9605	0.2679	145	0.2184	2812	X-RAY DIFFRACTION	100
1.9605-1.9943	0.2164	122	0.2053	2826	X-RAY DIFFRACTION	100
1.9943-2.0306	0.2089	146	0.1969	2798	X-RAY DIFFRACTION	100
2.0306-2.0697	0.2297	140	0.1904	2801	X-RAY DIFFRACTION	100
2.0697-2.1119	0.2194	132	0.1852	2823	X-RAY DIFFRACTION	100
2.1119-2.1578	0.2263	145	0.1697	2775	X-RAY DIFFRACTION	100
2.1578-2.208	0.1908	118	0.1659	2820	X-RAY DIFFRACTION	100
2.208-2.2632	0.1712	157	0.16	2782	X-RAY DIFFRACTION	100
2.2632-2.3244	0.1791	139	0.1501	2796	X-RAY DIFFRACTION	100
2.3244-2.3928	0.1605	149	0.1485	2815	X-RAY DIFFRACTION	100
2.3928-2.47	0.1841	167	0.1523	2758	X-RAY DIFFRACTION	100
2.47-2.5582	0.1837	153	0.1525	2815	X-RAY DIFFRACTION	100
2.5582-2.6606	0.2194	135	0.1609	2799	X-RAY DIFFRACTION	100
2.6606-2.7817	0.1854	142	0.1486	2815	X-RAY DIFFRACTION	100
2.7817-2.9283	0.1874	133	0.1564	2798	X-RAY DIFFRACTION	100
2.9283-3.1116	0.1611	121	0.1529	2845	X-RAY DIFFRACTION	100
3.1116-3.3517	0.165	165	0.1522	2806	X-RAY DIFFRACTION	100
3.3517-3.6886	0.1906	153	0.1423	2804	X-RAY DIFFRACTION	100
3.6886-4.2216	0.1525	168	0.1393	2792	X-RAY DIFFRACTION	100
4.2216-5.3157	0.1586	120	0.1541	2867	X-RAY DIFFRACTION	100
5.3157-34.8489	0.2286	154	0.2167	2869	X-RAY DIFFRACTION	100

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	7.421	1.4235	-4.0345	7.7246	-2.447	2.551	-0.0835	-0.5781	-0.4776	0.544	-0.1099	-0.0218	0.0933	0.292	0.2122	0.2895	0.0057	-0.0061	0.3712	0.0875	0.2492	-23.3684	-32.4366	-10.5895
2	3.1714	-1.6412	-2.5468	4.8826	1.2503	5.1474	-0.1199	-0.1717	-0.3326	0.4611	0.1156	0.4181	0.6864	-0.1992	0.1992	0.3229	-0.037	0.0094	0.2698	0.032	0.3761	-30.1443	-34.8053	-20.8235
3	6.6296	-3.073	-2.7683	3.1822	2.448	5.2389	-0.0203	-0.3546	0.0717	0.2617	0.0208	0.0352	-0.1631	-0.1302	0.0095	0.2756	-0.0211	0.0257	0.2831	0.0169	0.2313	-26.9525	-24.8247	-16.8728
4	2.5392	-1.8055	-0.2038	5.1907	1.894	5.2283	-0.0012	-0.2543	0.39	0.3409	0.0297	-0.3969	-0.2857	0.278	-0.0809	0.2314	-0.0788	-0.0032	0.2884	-0.0329	0.2967	-20.9357	-14.2506	-19.1941
5	2.6859	-1.5592	-0.4072	2.2105	0.8259	1.0223	0.1033	-0.0367	0.1167	0.1624	0.0328	0.0411	-0.1568	-0.0657	-0.148	0.3269	-0.0116	0.0377	0.2358	0.0115	0.2819	-36.2962	-13.0051	-21.7141
6	3.796	-1.666	1.501	2.4662	-0.3541	3.1786	0.0339	0.3404	-0.0737	-0.2164	-0.0873	0.0092	0.0413	0.1756	0.0186	0.2744	-0.0362	-0.0052	0.2618	-0.024	0.2723	-29.5738	-23.0377	-35.3159
7	4.6907	-0.7454	-3.717	3.3435	0.3926	6.5037	-0.0223	-0.6025	-0.2199	0.5778	0.043	0.4162	0.0812	0.2757	-0.0429	0.2634	-0.0454	0.0425	0.2372	0.0196	0.3136	-47.0141	-20.9964	-19.3309
8	6.423	0.1924	-5.0879	1.0093	-0.0763	4.2709	0.0199	0.4488	-0.1395	-0.0723	-0.0471	0.3848	-0.0705	-0.7542	0.1482	0.2707	-0.0203	-0.0229	0.3001	-0.025	0.3443	-48.2836	-26.7013	-33.3633
9	3.7331	0.4997	-1.7121	3.9474	-3.171	3.2123	-0.0246	-0.0491	-0.3273	-0.0075	0.0921	0.1354	0.4238	-0.1688	-0.06	0.3141	-0.022	-0.0312	0.2763	-0.0359	0.3898	-35.9273	-31.8822	-31.784
10	5.3892	0.5267	-0.4625	3.6317	-0.5378	1.8544	-0.1488	0.6222	0.1068	-0.4014	0.0924	0.4982	-0.1948	-0.3111	0.1017	0.4644	-0.0476	-0.1229	0.382	0.0129	0.3528	-40.7042	14.4923	-40.7936
11	6.0078	0.081	0.3922	9.7638	2.7004	4.8548	-0.2561	0.6014	-0.415	-0.715	-0.0345	0.4322	0.173	-0.24	0.1854	0.3669	-0.0821	0.0062	0.2983	-0.0176	0.2687	-34.8782	7.8909	-40.6756
12	3.1522	-1.311	-1.8861	7.3985	2.2236	5.8948	-0.1104	0.3669	-0.186	-0.4419	-0.013	-0.5183	0.0223	0.1668	0.0582	0.2673	-0.0549	0.0678	0.2984	-0.0189	0.3147	-24.598	1.6368	-37.3765
13	1.271	1.2689	1.7993	5.1216	3.2695	4.0655	-0.1135	0.152	-0.0126	-0.294	0.1504	-0.0527	-0.1863	0.1659	0.0669	0.3229	-0.0244	0.057	0.2756	0.0057	0.2965	-33.092	-4.9119	-33.9572
14	1.6254	1.4585	0.7773	7.4018	2.6142	2.4632	-0.0843	0.1802	-0.189	-0.4092	0.1265	0.1198	0.0545	0.4965	-0.0294	0.4291	0.0658	0.0178	0.4	0.0198	0.3182	-44.8219	-10.0552	-38.8251
15	2.432	2.1011	-0.4484	7.6725	-0.1222	2.9729	-0.1145	0.0177	0.0152	0.4021	0.0271	0.1308	-0.0029	0.0177	0.0942	0.2798	0.0086	0.0385	0.2451	-0.015	0.305	-37.5472	4.9214	-22.5124
16	3.4374	0.6082	2.6821	5.289	2.5998	7.1055	-0.059	0.3846	0.009	-0.789	-0.1332	0.3775	-0.2142	-0.132	0.1752	0.3366	0.0218	0.0088	0.2801	0.0033	0.3716	-50.9363	-5.4439	-39.325
17	4.0647	1.1542	4.0053	3.2223	3.1365	8.7701	0.0727	-0.261	0.0423	0.2829	-0.3478	0.865	0.3615	-0.9474	0.2206	0.3477	-0.0071	0.1037	0.3702	0.0013	0.5521	-55.4993	-1.5153	-25.3113
18	3.8829	0.4591	2.8913	4.431	1.2068	7.8658	-0.0659	0.2811	0.1965	-0.2777	0.1292	0.4831	-0.0352	-0.1967	0.1256	0.3315	0.0211	0.0206	0.3276	0.0068	0.4986	-47.6399	8.5723	-29.8789

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 46 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 132 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 133 through 177 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 178 through 200 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 201 through 245 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 246 through 278 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 279 through 304 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 4 through 61 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 62 through 82 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 83 through 132 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 133 through 159 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 160 through 177 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 178 through 200 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 201 through 245 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 246 through 278 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 279 through 309 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 524 molecules

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Yorodumi