PDB-5hss: Linalool dehydratase/isomerase: Ldi with monoterpene substrate

ID or keywords:

Entry

Database: PDB / ID: 5hss

Title

Linalool dehydratase/isomerase: Ldi with monoterpene substrate

Components

Linalool dehydratase/isomerase

Keywords

LYASE / Linalool dehydratase/isomerase / alpha6 alpha6 barrel fold / myrcene / geraniol

Function / homology

Function and homology information

linalool dehydratase / geraniol isomerase / monoterpene catabolic process / intramolecular hydroxytransferase activity / monoterpenoid metabolic process / hydro-lyase activity / periplasmic space
Similarity search - Function

Biological species

Castellaniella defragrans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.5 Å

Authors

Weidenweber, S. / Marmulla, R. / Harder, J. / Ermler, U.

Funding support

Germany, 1items

Citation

Journal: Febs Lett. / Year: 2016
Title: X-ray structure of linalool dehydratase/isomerase from Castellaniella defragrans reveals enzymatic alkene synthesis.
Authors: Weidenweber, S. / Marmulla, R. / Ermler, U. / Harder, J.

History

Deposition	Jan 26, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 18, 2016	Group: Database references
Revision 1.2	Oct 23, 2024	Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hss.cif.gz	730.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5hss.ent.gz	615.7 KB	Display	PDB format
PDBx/mmJSON format	5hss.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5hss_validation.pdf.gz	492.7 KB	Display	wwPDB validaton report
Full document	5hss_full_validation.pdf.gz	510.7 KB	Display
Data in XML	5hss_validation.xml.gz	63.4 KB	Display
Data in CIF	5hss_validation.cif.gz	85.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hs/5hss ftp://data.pdbj.org/pub/pdb/validation_reports/hs/5hss	HTTPS FTP

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Related structure data

Related structure data	5hlrC C: citing same article (ref.)
Similar structure data	5hlr-d 6tft-d 6tfn-2 5i3t-d 6t9h-2 5g1u-d 6t9h-1 6thm-d 6tfn-1 5g1v-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

Deposited unit

A: Linalool dehydratase/isomerase

B: Linalool dehydratase/isomerase

C: Linalool dehydratase/isomerase

D: Linalool dehydratase/isomerase

E: Linalool dehydratase/isomerase

hetero molecules

211 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	99.270, 106.290, 221.330
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Linalool dehydratase/isomerase / Geraniol isomerase / Linalool dehydratase-isomerase / Myrcene hydratase Mass: 41862.520 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Castellaniella defragrans (bacteria) / Gene: ldi / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: E1XUJ2, linalool dehydratase, geraniol isomerase
#2: Chemical	ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 Mass: 120.147 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₅H₁₂O₃ / Comment: precipitant*YM
#3: Chemical	ChemComp-64Z / Geraniol Mass: 154.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₈O
#4: Chemical	ChemComp-650 / Beta-Myrcene Mass: 138.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₈
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.79 Å³/Da / Density % sol: 55.9 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 550 MME, bicine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97928 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97928 Å / Relative weight: 1
Reflection	Resolution: 2.5→50 Å / Num. all: 81656 / Num. obs: 957382 / % possible obs: 99.8 % / Redundancy: 11.7 % / CC_1/2: 0.997 / R_sym value: 0.014 / Net I/av σ(I): 13.7 / Net I/σ(I): 13.7
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155)	refinement
XDS		data reduction
XDS		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.5→49.08 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.48

	R_factor	Num. reflection	% reflection
R_free	0.223	4029	4.94 %
R_work	0.1785	-	-
obs	0.1807	81564	99.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5→49.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14590	0	93	121	14804

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15122
X-RAY DIFFRACTION	f_angle_d	0.927	20541
X-RAY DIFFRACTION	f_dihedral_angle_d	10.439	8886
X-RAY DIFFRACTION	f_chiral_restr	0.054	2150
X-RAY DIFFRACTION	f_plane_restr	0.006	2662

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 (%)
2.4999-2.5293	0.4266	144	0.3726	2570	X-RAY DIFFRACTION	97
2.5293-2.5602	0.3111	136	0.2786	2646	X-RAY DIFFRACTION	100
2.5602-2.5926	0.3497	146	0.2624	2655	X-RAY DIFFRACTION	100
2.5926-2.6267	0.3086	136	0.2587	2625	X-RAY DIFFRACTION	100
2.6267-2.6627	0.3447	149	0.2919	2626	X-RAY DIFFRACTION	100
2.6627-2.7007	0.4007	126	0.333	2648	X-RAY DIFFRACTION	99
2.7007-2.741	0.3097	142	0.2664	2635	X-RAY DIFFRACTION	100
2.741-2.7838	0.3124	132	0.2537	2636	X-RAY DIFFRACTION	100
2.7838-2.8295	0.2825	145	0.2254	2645	X-RAY DIFFRACTION	100
2.8295-2.8782	0.2512	134	0.213	2683	X-RAY DIFFRACTION	100
2.8782-2.9306	0.2816	142	0.2221	2642	X-RAY DIFFRACTION	100
2.9306-2.9869	0.2948	156	0.2207	2627	X-RAY DIFFRACTION	100
2.9869-3.0479	0.2605	138	0.2064	2654	X-RAY DIFFRACTION	100
3.0479-3.1142	0.2479	135	0.2174	2666	X-RAY DIFFRACTION	100
3.1142-3.1866	0.2775	124	0.214	2666	X-RAY DIFFRACTION	100
3.1866-3.2663	0.2644	139	0.2107	2655	X-RAY DIFFRACTION	100
3.2663-3.3546	0.2648	136	0.2085	2683	X-RAY DIFFRACTION	100
3.3546-3.4532	0.2659	141	0.2281	2658	X-RAY DIFFRACTION	100
3.4532-3.5647	0.2769	151	0.1938	2648	X-RAY DIFFRACTION	100
3.5647-3.692	0.2392	141	0.1964	2669	X-RAY DIFFRACTION	100
3.692-3.8398	0.192	154	0.1686	2670	X-RAY DIFFRACTION	100
3.8398-4.0145	0.1925	135	0.1526	2660	X-RAY DIFFRACTION	99
4.0145-4.226	0.167	125	0.1356	2691	X-RAY DIFFRACTION	100
4.226-4.4906	0.1745	118	0.1299	2737	X-RAY DIFFRACTION	100
4.4906-4.8371	0.1696	122	0.1259	2731	X-RAY DIFFRACTION	100
4.8371-5.3233	0.19	137	0.1404	2717	X-RAY DIFFRACTION	100
5.3233-6.0924	0.1888	140	0.1586	2740	X-RAY DIFFRACTION	100
6.0924-7.671	0.1771	147	0.1513	2783	X-RAY DIFFRACTION	100
7.671-49.0897	0.1618	158	0.1294	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	7.8482	-7.1544	-0.9545	8.1883	-0.3538	8.627	0.1885	0.0826	0.6666	0.6129	-0.3814	-0.3482	-0.798	0.3754	0.2503	0.6685	-0.1244	0.036	0.3648	-0.0505	0.4378	88.8031	106.3606	85.053
2	4.5958	2.2973	-1.0824	6.2071	-1.2556	4.3126	0.0589	0.3862	-0.3274	-0.4544	-0.1996	0.3287	0.2697	-0.2446	0.1503	0.3618	0.0929	-0.0255	0.3741	-0.0713	0.385	76.1276	90.5326	73.0323
3	2.1511	-0.0187	0.32	4.6267	-0.6761	3.6552	0.1384	0.1105	-0.2041	0.2559	0.2104	0.8195	0.0096	-0.5161	-0.3312	0.3515	0.0512	0.1021	0.4321	0.0369	0.5861	65.4344	91.6318	83.4981
4	5.0451	-0.7154	1.2086	2.7043	-1.9725	5.6875	0.0934	-0.3693	-0.2397	0.6209	0.1759	0.8929	-0.2742	-0.404	-0.2229	0.6282	0.1078	0.3453	0.4948	0.0215	0.8163	58.7468	95.728	96.0253
5	2.2707	-0.7606	3.3979	9.2722	-0.5172	9.8725	0.1706	-1.4969	-0.3586	0.9205	-0.0752	1.0152	-0.6733	-0.6534	0.022	0.821	-0.0003	0.2198	0.7038	-0.0041	0.6147	70.9702	85.245	109.209
6	2.0702	0.8025	0.4141	2.2445	-1.1314	2.2809	0.1763	-0.2573	0.086	0.6601	-0.1009	0.1387	-0.3012	-0.0085	-0.0705	0.5734	-0.0092	0.0325	0.3455	-0.0752	0.3449	82.6442	95.4089	94.0699
7	4.0605	0.2775	0.5725	3.7319	1.2149	3	0.117	-0.0275	-0.0523	0.158	0.0644	-0.2393	-0.0798	-0.0144	-0.1853	0.4782	0.0206	0.0364	0.3457	-0.0432	0.3524	71.1333	64.253	102.9492
8	5.4637	3.6836	1.1457	8.6335	0.8343	4.9635	-0.0434	0.1298	0.3174	0.2028	-0.0908	0.9175	-0.0794	-0.7763	0.1414	0.4809	0.0406	0.1399	0.4661	-0.0759	0.469	55.2811	58.1441	106.9925
9	7.7733	-5.227	-4.0542	8.3926	5.2026	3.5821	-0.3501	0.1243	-0.8055	0.9669	-0.1717	0.5671	0.5379	-0.3721	0.5449	0.8061	-0.0226	0.14	0.5406	-0.0293	0.5256	62.4755	41.9075	108.3148
10	2.227	-0.3185	-0.1223	4.1882	-0.0499	2.8617	-0.0303	-0.2093	-0.0343	0.6239	0.1812	-0.3951	0.435	0.4471	-0.1355	0.6888	0.1136	-0.1045	0.5694	-0.0908	0.3849	80.3064	52.1466	109.9597
11	7.2976	5.2651	2.8856	6.2963	2.8643	2.3505	-0.3619	0.8415	-0.7571	-0.8358	0.4741	-0.9736	0.2101	0.6053	-0.1538	0.5938	-0.0063	0.092	0.4357	-0.0772	0.5551	89.458	34.7187	37.7025
12	2.1267	-0.1278	0.7075	3.9054	-0.6782	1.611	-0.0942	-0.1602	0.1407	-0.0811	0.135	0.6514	0.0739	-0.3969	-0.0335	0.3223	-0.0794	-0.0485	0.4887	-0.0064	0.49	66.6042	46.5629	45.7819
13	5.6509	3.7337	0.4716	6.7606	-0.1699	0.5612	-0.1742	0.1879	0.4472	-0.9635	0.0229	0.7212	0.1516	-0.283	0.1841	0.5725	-0.0314	-0.2063	0.5653	0.0575	0.4951	68.3451	59.5259	28.5982
14	2.4884	0.5555	-0.871	3.5536	-0.7128	2.4583	-0.01	0.2248	-0.007	-0.4987	0.0337	-0.0386	0.1308	0.0886	-0.0199	0.3684	-0.0011	-0.0033	0.3618	-0.0562	0.3176	84.8246	49.288	35.7329
15	4.4023	-3.8794	4.8312	5.9751	-3.4941	5.5332	0.0917	0.7491	0.2452	-0.5647	0.3436	-0.1886	-0.4197	0.5752	-0.33	0.5062	-0.1223	0.0778	0.6296	-0.0088	0.3911	91.9657	87.8775	35.1953
16	0.9272	-1.1737	-1.8887	2.9024	1.661	5.656	0.0881	-0.1523	-0.2169	0.1548	0.0465	0.454	0.4728	0.106	-0.1221	0.3342	-0.0269	-0.0875	0.4055	0.0239	0.49	77.2745	72.9617	46.1806
17	2.1545	0.0439	-0.7059	2.4692	0.3074	8.0467	-0.0894	-0.0375	0.0398	-0.0634	-0.0138	0.5847	-0.1746	-0.6623	0.0706	0.3076	-0.0017	-0.1045	0.4823	0.0538	0.5893	68.2556	82.9627	48.9009
18	1.8539	-1.519	-2.4652	3.5672	2.0053	5.1919	-0.035	0.183	-0.1625	-0.3336	-0.2633	0.9642	-0.327	-0.9327	0.3334	0.3378	0.0391	-0.176	0.6113	-0.0093	0.7332	60.4882	89.8582	44.5863
19	6.8936	0.9573	5.4625	2.0551	1.7236	8.1133	-0.0834	-0.2457	0.4818	-0.1987	-0.0204	0.4873	-0.5728	-0.7	0.1229	0.4249	0.09	-0.0313	0.3862	0.0021	0.5731	68.1948	102.855	53.9038
20	3.8464	-1.0665	-1.0481	4.445	0.4816	4.2005	-0.0463	-0.0835	0.2753	-0.1226	0.1883	-0.2061	-0.326	0.1995	-0.1381	0.3243	-0.0752	-0.027	0.2841	-0.0092	0.3258	86.9952	99.0698	50.3853
21	3.2011	1.3914	-1.1152	5.4488	5.4457	7.9973	-0.1279	-0.2923	-0.6151	0.3098	0.4614	-0.4613	0.1692	1.0657	-0.3961	0.3186	0.0879	-0.0432	0.4473	0.0473	0.3855	90.7436	77.8339	48.7206
22	4.6924	-0.369	-3.3121	6.3647	1.8838	4.9314	0.1779	0.4938	0.1012	-0.7903	0.1833	0.3682	-0.189	-0.2563	-0.3464	0.371	-0.0656	-0.0532	0.3657	0.0284	0.4014	77.4694	89.9006	38.9265
23	4.7881	4.2524	-4.6118	3.8262	-4.0583	4.4633	0.0272	-0.2677	-0.6118	0.3898	-0.2686	-0.133	0.2081	0.6245	0.2317	0.5537	0.0445	-0.0317	0.4834	0.0099	0.5016	85.3247	19.7936	88.0972
24	2.7133	-1.0587	2.2	0.8674	-1.8172	3.891	-0.0408	-0.1337	0.2808	0.1787	0.013	0.1746	-0.2509	0.0283	0.026	0.4673	-0.0262	-0.0103	0.4091	-0.0956	0.535	73.1951	40.1764	87.0182
25	2.23	-0.7269	1.0469	4.28	-2.1163	5.2012	-0.0657	0.0337	0.2941	-0.112	-0.0284	0.3328	-0.1728	-0.6561	0.1144	0.343	0.013	0.0117	0.486	-0.0838	0.6144	64.1395	34.9978	78.0853
26	4.7166	-1.283	3.4092	3.7939	-2.3513	3.2346	-0.1879	-0.2557	0.1095	0.2296	0.2398	0.7889	0.1909	-1.1776	-0.0514	0.4092	-0.0258	0.0181	0.6225	-0.1273	0.7011	55.4142	27.8728	76.8526
27	6.8958	1.6804	-4.5661	2.1265	-0.829	6.4769	-0.1477	0.665	-0.0009	-0.3699	0.2351	0.4268	0.3624	-0.5291	-0.1065	0.3793	-0.0427	-0.1125	0.4548	-0.0187	0.4967	63.7101	22.1089	62.1614
28	3.4043	1.2061	0.4601	2.222	-0.3773	3.4621	-0.0299	0.1171	-0.1804	-0.1643	-0.0782	-0.1415	0.2676	0.2128	0.1119	0.461	0.0414	0.0311	0.3232	-0.0105	0.4413	81.9724	20.716	68.9009
29	1.9092	-2.4094	0.4367	3.5779	-0.6454	6.5195	-0.1671	-0.1463	0.3054	0.0513	0.2426	-0.3122	-0.3265	0.6321	-0.0305	0.393	-0.0222	-0.0463	0.3313	-0.064	0.6156	86.4864	36.1744	83.3343
30	7.4531	0.9137	-1.8175	7.3529	-1.8277	2.4226	0.1483	-0.9422	-0.6631	0.6947	-0.1563	0.5792	0.5837	-0.1424	-0.1437	0.4996	-0.0431	0.0181	0.5451	-0.0195	0.412	71.1861	22.2823	83.1148

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 59 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 60 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 210 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 211 through 237 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 238 through 366 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 122 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 123 through 162 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 163 through 237 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 238 through 366 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 24 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 25 through 162 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 163 through 237 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 238 through 365 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 24 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 25 through 59 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 60 through 122 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 123 through 162 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 163 through 237 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 238 through 319 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 320 through 341 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 342 through 365 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 1 through 24 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 25 through 59 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 60 through 122 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 123 through 162 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 163 through 237 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 238 through 319 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 320 through 341 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 342 through 366 )

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News

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