PDB-5hlr: Linalool dehydratase/isomerase: Ldi-apo

ID or keywords:

Entry

Database: PDB / ID: 5hlr

Title

Linalool dehydratase/isomerase: Ldi-apo

Components

Linalool dehydratase/isomerase

Keywords

ISOMERASE / Linalool dehydratase/isomerase / alpha6 alpha6 barrel fold / anaerobic degradation / monoterpene

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: 1.911 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 15, 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	Sep 6, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 9, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5hlr.cif.gz	725.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5hlr.ent.gz	610 KB	Display	PDB format
PDBx/mmJSON format	5hlr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hl/5hlr ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hlr	HTTPS FTP

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Related structure data

Related structure data	5hssC C: citing same article (ref.)
Similar structure data	6tfn-2 6t9h-1 6t9h-2 5g1u-d 6tfn-1 5hss-d 5g1v-d 6tft-d 5i3t-d 5g1w-d 6thm-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

210 kDa, 5 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)	99.960, 106.750, 223.110
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: inhibitor, precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 580 / 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: 2.84 Å³/Da / Density % sol: 56.74 %
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: 1.00002 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 183334 / % possible obs: 99.9 % / Redundancy: 5.9 % / R_sym value: 0.098 / Net I/σ(I): 10.5
Reflection shell	Resolution: 1.9→2 Å / Num. unique all: 25877 / R_sym value: 0.71

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
SHARP		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 1.911→49.5 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.31

	R_factor	Num. reflection	% reflection
R_free	0.2246	9187	5.01 %
R_work	0.1895	-	-
obs	0.1912	183334	99.27 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.911→49.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14590	0	40	580	15210

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	15074
X-RAY DIFFRACTION	f_angle_d	1.172	20478
X-RAY DIFFRACTION	f_dihedral_angle_d	13.56	5433
X-RAY DIFFRACTION	f_chiral_restr	0.053	2150
X-RAY DIFFRACTION	f_plane_restr	0.006	2652

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 (%)
1.9111-1.9328	0.3271	253	0.2749	4789	X-RAY DIFFRACTION	82
1.9328-1.9556	0.329	285	0.2666	5792	X-RAY DIFFRACTION	100
1.9556-1.9794	0.3007	320	0.2525	5728	X-RAY DIFFRACTION	100
1.9794-2.0045	0.2746	294	0.247	5814	X-RAY DIFFRACTION	100
2.0045-2.0309	0.2857	295	0.2428	5757	X-RAY DIFFRACTION	100
2.0309-2.0587	0.2965	310	0.237	5786	X-RAY DIFFRACTION	100
2.0587-2.0881	0.2826	322	0.2337	5795	X-RAY DIFFRACTION	100
2.0881-2.1193	0.2958	333	0.2289	5742	X-RAY DIFFRACTION	100
2.1193-2.1524	0.2634	312	0.2143	5756	X-RAY DIFFRACTION	100
2.1524-2.1877	0.2626	304	0.2123	5813	X-RAY DIFFRACTION	100
2.1877-2.2254	0.2511	299	0.2062	5847	X-RAY DIFFRACTION	100
2.2254-2.2658	0.2312	343	0.1986	5727	X-RAY DIFFRACTION	100
2.2658-2.3094	0.2368	281	0.1981	5823	X-RAY DIFFRACTION	100
2.3094-2.3566	0.2276	307	0.1896	5821	X-RAY DIFFRACTION	100
2.3566-2.4078	0.23	303	0.1907	5797	X-RAY DIFFRACTION	100
2.4078-2.4638	0.2362	322	0.192	5794	X-RAY DIFFRACTION	100
2.4638-2.5254	0.2311	313	0.1936	5815	X-RAY DIFFRACTION	100
2.5254-2.5937	0.2381	323	0.1888	5791	X-RAY DIFFRACTION	100
2.5937-2.67	0.2518	306	0.1907	5848	X-RAY DIFFRACTION	100
2.67-2.7562	0.2335	307	0.1911	5826	X-RAY DIFFRACTION	100
2.7562-2.8547	0.2348	297	0.1931	5818	X-RAY DIFFRACTION	100
2.8547-2.969	0.2683	318	0.2097	5857	X-RAY DIFFRACTION	100
2.969-3.1041	0.2438	310	0.2157	5824	X-RAY DIFFRACTION	100
3.1041-3.2677	0.2424	296	0.218	5859	X-RAY DIFFRACTION	100
3.2677-3.4724	0.2346	305	0.2066	5909	X-RAY DIFFRACTION	100
3.4724-3.7404	0.2327	325	0.1937	5866	X-RAY DIFFRACTION	100
3.7404-4.1167	0.1865	302	0.1628	5926	X-RAY DIFFRACTION	100
4.1167-4.7119	0.1708	270	0.1476	5991	X-RAY DIFFRACTION	100
4.7119-5.935	0.1886	297	0.1587	6017	X-RAY DIFFRACTION	100
5.935-49.4525	0.1701	335	0.1588	6190	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	4.8112	-3.9188	-0.634	3.6886	-0.1124	2.894	0.035	0.1038	0.1145	0.1237	-0.2022	-0.0613	-0.1754	0.1271	0.1976	0.3835	-0.0735	-0.0077	0.255	-0.0105	0.2963	89.4426	106.7914	85.7007
2	2.1551	1.7107	-0.2893	2.9354	-0.9704	2.2485	-0.0515	0.2383	-0.09	-0.2936	-0.0141	0.1093	0.1284	-0.1301	0.0786	0.2221	0.0469	0.001	0.2794	-0.0436	0.2608	76.7432	90.8671	73.6676
3	1.4753	0.5755	0.0659	5.0034	-1.5322	1.641	0.047	0.0258	-0.1186	0.1601	0.0605	0.4096	0.0156	-0.3015	-0.1406	0.262	0.0224	0.0194	0.3551	-0.0453	0.343	66.0655	91.8722	84.1813
4	2.3733	-0.7223	0.6816	2.4494	-1.6238	4.0673	0.0781	-0.1714	-0.202	0.4352	0.1349	0.5625	-0.1842	-0.1571	-0.1759	0.376	0.0356	0.1308	0.3441	-0.0402	0.4657	59.4055	95.9565	96.8449
5	7.1429	0.2474	0.5192	5.045	0.2326	4.5132	0.0573	-0.6837	-0.1667	0.8229	-0.0773	0.3064	-0.0906	-0.2089	0.0901	0.5194	-0.0127	0.1121	0.4051	-0.0157	0.2792	71.8045	85.3094	110.1479
6	1.1834	0.2725	0.1978	1.3544	-0.1387	1.0043	0.1099	-0.0763	0.0495	0.2723	-0.1027	0.0246	-0.2095	-0.0188	-0.0241	0.3457	-0.0268	-0.0042	0.2155	-0.0455	0.2062	83.4142	95.7422	94.8274
7	1.9932	-0.0372	0.4256	2.6206	1.022	2.1857	0.1083	-0.0365	-0.0332	0.1646	0.0109	0.0585	0.082	-0.0217	-0.0884	0.3117	0.0215	0.0219	0.2619	-0.0263	0.2469	71.755	64.4795	103.7866
8	2.8321	1.5379	0.5798	6.115	1.0205	2.451	-0.1025	0.1717	0.1131	-0.0378	-0.0891	0.6917	-0.0317	-0.3768	0.1777	0.3334	0.0258	0.1046	0.395	-0.0694	0.4267	55.7496	58.5065	107.5479
9	3.3558	-2.2221	-1.7775	3.7482	2.2894	1.5021	-0.2226	0.1431	-0.5056	0.6638	-0.0795	0.434	0.3505	-0.1914	0.267	0.4393	-0.0081	0.1238	0.3166	-0.0251	0.3299	62.8644	42.1386	108.9404
10	1.0464	-0.5011	0.2635	2.9804	0.1924	1.2493	-0.0818	-0.1309	-0.016	0.4042	0.1239	-0.1289	0.2081	0.2081	-0.0576	0.3938	0.0782	-0.0442	0.3291	-0.055	0.2028	80.8496	52.2714	110.9155
11	4.8381	0.1786	1.5529	4.739	0.0033	7.133	0.0943	0.5621	-0.4391	-0.6997	0.017	-0.4007	0.3926	0.3881	-0.0982	0.3173	0.0451	0.0685	0.2098	-0.0218	0.2901	90.2204	34.8143	37.8614
12	0.8325	0.0966	0.238	1.9834	-0.502	1.0283	0.0142	-0.093	0.072	-0.0347	0.0558	0.375	-0.0091	-0.1752	-0.0699	0.2511	-0.0488	-0.02	0.342	-0.0132	0.3248	67.1935	46.5488	46.2465
13	4.0842	2.6776	1.0456	4.3487	-0.1594	0.8135	-0.0761	0.073	0.4306	-0.5068	-0.0574	0.4633	0.1246	-0.1076	0.1113	0.4002	-0.0183	-0.0824	0.361	-0.0087	0.3268	68.8428	59.6852	29.0571
14	0.9418	0.2115	-0.2787	2.1987	-0.6152	1.5141	0.0138	0.1327	0.0255	-0.2565	-0.039	-0.0908	0.1189	0.0588	0.0318	0.2513	0.0043	0.0096	0.2558	-0.0236	0.2199	85.4509	49.4224	36.0919
15	4.3948	-2.8589	3.8386	7.0499	-2.6734	3.4142	-0.0815	0.3327	0.3174	-0.3106	0.0599	-0.1033	-0.2027	0.1284	-0.0317	0.3041	-0.0694	0.0569	0.3787	-0.0129	0.1985	92.4476	88.1845	35.4595
16	1.5814	0.0119	-0.977	1.2689	0.4585	2.3273	0.0018	-0.0709	-0.1103	0.0159	0.0013	0.2336	0.1589	0.0241	0.0137	0.2148	0.0281	-0.0275	0.2567	-0.0001	0.3054	77.822	73.2102	46.5623
17	1.4552	0.4246	0.0891	1.5957	-0.2242	3.9441	0.0108	-0.06	0.0643	0.0011	-0.1259	0.3189	-0.2794	-0.5174	0.1001	0.2043	0.0205	-0.0397	0.2914	-0.0176	0.3631	68.696	83.1274	49.3734
18	2.4786	-1.8267	-2.0105	4.3726	1.837	3.4687	-0.1281	-0.0541	-0.0729	0.1404	-0.1463	0.515	-0.0084	-0.3699	0.2448	0.2808	0.017	-0.0871	0.3956	-0.0377	0.4424	60.896	90.1344	45.0494
19	3.4042	0.3011	2.8732	1.3575	0.6726	4.2396	-0.0598	-0.265	0.1615	-0.1524	0.0126	0.1936	-0.1518	-0.4518	0.0262	0.2929	0.058	-0.0276	0.3166	-0.0253	0.3488	68.6383	103.0826	54.472
20	2.7642	-0.0882	0.2515	1.7564	-0.0646	2.3592	0.0088	-0.0321	0.1172	-0.0911	0.0497	0.0383	-0.2013	0.1244	-0.0497	0.2583	-0.0393	-0.0006	0.2388	-0.0326	0.2381	87.4371	99.3956	50.8312
21	0.8758	-0.6808	-1.1632	4.689	3.9248	3.8071	-0.2236	-0.161	-0.2635	0.2686	0.4458	-0.1434	0.3757	0.3808	-0.21	0.2507	0.0338	-0.017	0.3449	-0.0149	0.2625	91.3086	78.0882	48.8957
22	3.8285	0.7426	-0.3302	1.0926	1.28	3.7678	0.0714	0.3449	-0	-0.6281	0.1035	0.3851	-0.2152	-0.09	-0.0991	0.283	-0.0192	-0.073	0.1871	0.0034	0.2515	77.9302	90.1557	39.3262
23	2.5064	2.04	-3.4855	5.7758	-0.5448	6.8322	-0.0875	-0.4826	-0.4757	0.2793	-0.0971	-0.0597	0.364	0.4601	0.099	0.345	0.0529	-0.0043	0.2734	0.0388	0.2948	85.8294	19.6355	88.8577
24	2.3307	-1.0308	1.5309	1.596	-1.0487	2.8886	-0.2116	-0.066	0.2487	0.2168	0.0083	0.1482	-0.2105	-0.1163	0.1722	0.301	-0.0018	-0.0019	0.2612	-0.0717	0.342	73.7651	40.2002	87.6656
25	1.9792	-0.4164	-0.2744	2.2468	-1.0967	2.6858	-0.0063	0.0804	0.2126	-0.1823	-0.0169	0.1809	0.0729	-0.2674	0.0115	0.2608	-0.0298	-0.0105	0.3255	-0.0774	0.42	64.64	35.1022	78.6527
26	2.7963	-0.6428	2.9519	1.7736	0.0213	6.3499	0.0053	-0.2477	0.2571	0.0056	-0.0268	0.4899	0.1776	-0.5805	0.0683	0.2794	-0.0514	0.0106	0.3858	-0.063	0.4901	55.8914	28.0251	77.3426
27	3.142	0.8975	-2.0949	0.7911	-1.0974	3.7014	-0.0401	0.2399	0.117	-0.1234	0.1668	0.2991	0.2535	-0.1847	-0.1234	0.3211	-0.0623	-0.0393	0.2937	-0.0062	0.3819	64.343	22.1733	62.5527
28	1.973	0.5664	-0.0817	1.2014	-0.4771	1.9106	-0.0411	0.0474	-0.1753	-0.0525	-0.0071	0.0225	0.2475	0.0591	0.0369	0.2899	0.0259	0.0157	0.2269	-0.0254	0.2597	82.6583	20.7633	69.5195
29	1.4653	-0.5841	0.217	1.9355	0.8009	2.1936	-0.1227	-0.0504	0.4085	-0.0831	0.0518	-0.1467	-0.6363	0.3767	0.0258	0.3069	-0.0214	-0.0036	0.2811	-0.0331	0.3161	87.119	36.1626	84.1485
30	4.9611	0.2953	-0.4164	3.7708	-0.4333	3.1612	0.0465	-0.3608	-0.228	0.2594	-0.03	0.4716	0.3962	-0.2066	-0.0661	0.3391	-0.0155	0.0246	0.2988	-0.0247	0.3061	71.7088	22.3158	83.6754

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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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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+About Yorodumi

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-Aug 12, 2020. Covid-19 info

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Download

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Validation report

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi