PDB-5nx7: Crystal structure of 1,8-cineole synthase from Streptomyces clavu...

ID or keywords:

Entry

Database: PDB / ID: 5nx7

Title

Crystal structure of 1,8-cineole synthase from Streptomyces clavuligerus in complex with 2-fluoroneryl diphosphate and 2-fluorogeranyl diphosphate

Components

Pentalenene synthase

Keywords

LYASE / terpene synthase / 1 / 8-cineole / monoterpenoid / Eucalyptol

Function / homology

Function and homology information

1,8-cineole synthase / 1,8-cineole synthase activity / geranyl diphosphate metabolic process / magnesium ion binding
Similarity search - Function

Biological species

Streptomyces clavuligerus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.51 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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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	5nx7.cif.gz	292.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5nx7.ent.gz	236.3 KB	Display	PDB format
PDBx/mmJSON format	5nx7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5nx7_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	5nx7_full_validation.pdf.gz	2.2 MB	Display
Data in XML	5nx7_validation.xml.gz	33.2 KB	Display
Data in CIF	5nx7_validation.cif.gz	51.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/5nx7 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/5nx7	HTTPS FTP

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Related structure data

Related structure data	5nx4C 5nx5C 5nx6C 1ps1S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6d0v-d 5nx6-d 6aqj-d 4huz-1 1ojm-d 6dz4-d 6xnc-d 6xt0-d 1wbj-d 3mgu-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 (1)

Deposited unit

A: Pentalenene synthase

B: Pentalenene synthase

hetero molecules

77.7 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)	60.745, 60.826, 64.258
Angle α, β, γ (deg.)	92.67, 89.98, 101.77
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 2 molecules AB

#1: Protein	Pentalenene synthase / 1 / 8-cineole synthase Mass: 37774.359 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_p0982, SSCG_00536 / Production host: Escherichia coli (E. coli) / References: UniProt: B5GMG2, pentalenene synthase

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Non-polymers , 6 types, 836 molecules

#2: 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.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₉FO₇P₂
#3: Chemical	ChemComp-LA6 / (2E)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate Mass: 332.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₉FO₇P₂
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-9D2 / 2-ethyl-2-(hydroxymethyl)propane-1,3-diol Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₃
#6: Chemical	ChemComp-NDS / ETHYL DIMETHYL AMMONIO PROPANE SULFONATE Mass: 195.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₇NO₃S
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 822 / 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: 3.07 Å³/Da / Density % sol: 59.98 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate), 0.1 M Buffer System 5 (BES, Triethanolamine) pH 7.5, 50 % v/v Precipitant Mix 8 (10% w/v PEG 20000, 50% ...Details: 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate), 0.1 M Buffer System 5 (BES, Triethanolamine) pH 7.5, 50 % v/v Precipitant Mix 8 (10% w/v PEG 20000, 50% w/v Trimethyl propane, 2% w/v NDSB 195)

Crystal

Density Matthews: 3.07 Å³/Da / Density % sol: 59.98 %

Crystal grow

Temperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 90 mM LiNaK (0.3 M Lithium sulfate, 0.3 M Sodium sulfate, 0.3 M Potassium sulfate), 0.1 M Buffer System 5 (BES, Triethanolamine) pH 7.5, 50 % v/v Precipitant Mix 8 (10% w/v PEG 20000, 50% ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 15, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.506→64.19 Å / Num. obs: 136704 / % possible obs: 95.9 % / Redundancy: 2 % / R_merge(I) obs: 0.035 / R_sym value: 0.032 / Net I/σ(I): 10
Reflection shell	Resolution: 1.51→1.53 Å / Redundancy: 2 % / R_merge(I) obs: 0.315 / Mean I/σ(I) obs: 2.1 / % possible all: 93.4

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Processing

Software

Name	Version	Classification
PHENIX	(DEV_2621: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1PS1

1ps1

Resolution: 1.51→43.42 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.77

	R_factor	Num. reflection	% reflection
R_free	0.174	7052	5.16 %
R_work	0.149	-	-
obs	0.151	136690	95.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.51→43.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4950	0	128	822	5900

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	5454
X-RAY DIFFRACTION	f_angle_d	0.956	7480
X-RAY DIFFRACTION	f_dihedral_angle_d	10.655	3214
X-RAY DIFFRACTION	f_chiral_restr	0.051	785
X-RAY DIFFRACTION	f_plane_restr	0.008	987

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 (%)
1.5055-1.5226	0.2519	205	0.2296	4315	X-RAY DIFFRACTION	94
1.5226-1.5405	0.2498	237	0.2301	4193	X-RAY DIFFRACTION	94
1.5405-1.5593	0.2276	212	0.2141	4314	X-RAY DIFFRACTION	94
1.5593-1.5791	0.2135	224	0.2064	4167	X-RAY DIFFRACTION	94
1.5791-1.5998	0.2344	216	0.2068	4304	X-RAY DIFFRACTION	94
1.5998-1.6217	0.2203	219	0.2073	4219	X-RAY DIFFRACTION	95
1.6217-1.6449	0.2008	205	0.1904	4361	X-RAY DIFFRACTION	95
1.6449-1.6695	0.225	226	0.196	4230	X-RAY DIFFRACTION	94
1.6695-1.6956	0.2106	221	0.1866	4309	X-RAY DIFFRACTION	95
1.6956-1.7234	0.2444	251	0.1859	4227	X-RAY DIFFRACTION	95
1.7234-1.7531	0.2066	241	0.1749	4294	X-RAY DIFFRACTION	95
1.7531-1.785	0.2049	266	0.1675	4341	X-RAY DIFFRACTION	96
1.785-1.8193	0.1923	216	0.1604	4236	X-RAY DIFFRACTION	96
1.8193-1.8564	0.1734	229	0.1645	4346	X-RAY DIFFRACTION	96
1.8564-1.8968	0.1869	274	0.1546	4280	X-RAY DIFFRACTION	96
1.8968-1.9409	0.1844	272	0.1565	4249	X-RAY DIFFRACTION	96
1.9409-1.9894	0.1471	290	0.1553	4261	X-RAY DIFFRACTION	96
1.9894-2.0432	0.1577	254	0.1449	4337	X-RAY DIFFRACTION	96
2.0432-2.1034	0.164	275	0.1395	4358	X-RAY DIFFRACTION	96
2.1034-2.1712	0.181	214	0.1401	4332	X-RAY DIFFRACTION	96
2.1712-2.2488	0.1449	213	0.1348	4395	X-RAY DIFFRACTION	97
2.2488-2.3389	0.1446	211	0.1266	4402	X-RAY DIFFRACTION	97
2.3389-2.4453	0.147	277	0.1257	4301	X-RAY DIFFRACTION	97
2.4453-2.5742	0.1432	235	0.129	4334	X-RAY DIFFRACTION	97
2.5742-2.7355	0.1602	222	0.1351	4418	X-RAY DIFFRACTION	98
2.7355-2.9467	0.1632	202	0.1383	4432	X-RAY DIFFRACTION	97
2.9467-3.2431	0.165	200	0.1434	4440	X-RAY DIFFRACTION	98
3.2431-3.7122	0.1691	247	0.1302	4399	X-RAY DIFFRACTION	98
3.7122-4.6761	0.1452	247	0.12	4447	X-RAY DIFFRACTION	98
4.6761-43.4378	0.2201	251	0.1836	4397	X-RAY DIFFRACTION	98

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	1.7885	0.2712	0.6973	6.337	0.4847	1.1031	0.005	0.0954	-0.0244	-0.2923	-0.0548	-0.0293	0.0501	0.0449	0.0257	0.1603	-0.0144	0.0303	0.1384	0.0137	0.0982	-9.2387	-13.1837	11.1217
2	5.6791	1.0308	0.3421	3.0181	-0.123	5.8814	-0.0882	-0.2115	0.0662	0.0587	0.053	-0.1802	-0.0303	0.2139	0.0307	0.0848	-0.0347	-0.0012	0.137	0.0044	0.1461	7.003	-3.255	23.3341
3	2.7877	0.0571	-0.5407	1.2101	-0.2894	2.3081	-0.0118	-0.6133	-0.0834	0.204	-0.0433	-0.1177	0.0363	0.2976	0.0671	0.1422	-0.0227	-0.0119	0.2333	0.006	0.1379	-2.3826	-7.7408	33.7223
4	3.9747	-0.9596	1.2402	3.7027	-0.4775	2.9255	0.0633	-0.4557	-0.5746	0.1241	-0.0646	-0.3982	0.5396	0.3368	0.0114	0.2945	0.0382	0.0122	0.2773	0.1042	0.2583	-5.4216	-20.535	38.2678
5	6.2035	-1.0154	2.8032	2.5431	-1.8241	8.658	-0.7694	-0.4277	-0.1787	1.2832	0.2129	-0.048	0.4551	0.0062	0.4526	0.6387	-0.0207	0.0569	0.2834	0.0378	0.2873	-7.5467	-30.7864	30.3648
6	1.409	-1.0736	-0.7039	2.2351	0.9686	1.3013	-0.0762	-0.1709	-0.0875	0.167	0.1012	-0.1265	0.1955	0.067	-0.024	0.1637	-0.0134	-0.0116	0.1377	0.0184	0.115	-9.7002	-21.5334	25.1787
7	7.546	-6.5427	-2.5733	6.3106	2.4516	1.4887	-0.0094	0.0029	-0.2424	0.0226	-0.0098	0.1954	0.073	-0.0801	0.0786	0.1425	-0.0394	0.0108	0.1146	0.0117	0.1543	-19.433	-24.2476	17.881
8	5.6625	-0.5021	-0.9505	1.5762	-0.009	1.2851	0.0911	-0.1561	0.0436	-0.0319	-0.0409	-0.1902	-0.0334	0.083	-0.0105	0.1288	-0.0286	-0.0047	0.0813	0.0043	0.0761	-10.8894	-12.053	19.8425
9	7.1066	1.5269	-0.5058	1.8133	-0.8347	1.0384	-0.0345	-0.2814	0.0867	0.0878	-0.0066	0.0422	-0.0223	-0.0654	0.0168	0.1535	-0.0089	0.001	0.1367	-0.0264	0.0929	-27.0067	1.2907	16.5587
10	2.9068	2.8297	-0.6967	4.916	-2.3453	5.5862	0.0617	0.0821	0.0733	0.0867	-0.1779	-0.2677	-0.1918	0.2907	0.1064	0.1826	0.0021	0.0046	0.0827	-0.0044	0.1552	-16.7793	16.2028	4.5711
11	1.092	-0.8223	0.2015	3.9355	-0.0836	1.8446	0.0501	0.0519	0.0928	-0.1354	-0.0905	0.0423	-0.1456	-0.059	0.0362	0.1164	-0.0173	0.0144	0.1015	-0.0003	0.1139	-23.2903	12.7623	3.0344
12	1.7095	-0.5041	0.1678	3.4441	1.0469	3.0876	0.0242	0.2391	0.137	-0.4973	-0.1159	0.0979	-0.4277	-0.1336	0.101	0.2632	0.0065	0.0143	0.1533	0.0064	0.1167	-23.375	9.7288	-13.6125
13	2.1129	1.2498	-0.9446	1.2575	0.0698	3.11	0.0958	0.0949	0.2881	-0.1759	-0.1445	0.4416	-0.0421	-0.6536	0.0638	0.218	-0.0027	-0.036	0.3274	-0.0423	0.2246	-36.7703	2.0469	-8.4688
14	2.6465	-1.039	-1.0892	1.1369	0.4785	1.4145	0.1116	0.195	0.1149	-0.1486	-0.0728	0.1305	-0.0158	-0.205	-0.0312	0.1581	-0.0215	-0.0223	0.151	0.0093	0.1332	-35.0812	-0.8711	2.4179
15	4.7658	-4.9132	-2.3162	4.7133	2.2498	0.8616	-0.0018	0.0049	-0.1741	-0.0336	0.0027	0.2026	0.0965	-0.065	0.0833	0.1636	-0.0184	0.002	0.1591	-0.0078	0.208	-36.1681	-10.5916	10.1847
16	2.0443	-1.1238	-0.2691	4.3047	0.6931	1.4341	0.0046	-0.0296	0.1549	-0.097	0.0033	0.0831	-0.0603	-0.0204	0.0347	0.0947	-0.0321	-0.0076	0.1025	0.0077	0.0763	-25.7636	-0.2914	7.7765

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 4 THROUGH 19 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 20 THROUGH 49 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 50 THROUGH 134 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 135 THROUGH 160 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 161 THROUGH 177 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 178 THROUGH 248 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 249 THROUGH 281 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 282 THROUGH 330 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 4 THROUGH 19 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 20 THROUGH 33 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 34 THROUGH 84 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 85 THROUGH 134 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 135 THROUGH 176 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 177 THROUGH 248 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 249 THROUGH 280 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 281 THROUGH 330 )

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Protein , 1 types, 2 molecules AB

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Non-polymers , 6 types, 836 molecules

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