PDB-6tfn: Linalool Dehydratase Isomerase in complex with Myrcene

ID or keywords:

Entry

Database: PDB / ID: 6tfn

Title

Linalool Dehydratase Isomerase in complex with Myrcene

Components

Linalool dehydratase-isomerase protein LDI

Keywords

LYASE / Alkene / Alkenol / Hydratase

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 65Phen (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.18 Å

Authors

Cuetos, A. / Zukic, E. / Danesh-Azari, H.R. / Grogan, G.

Funding support

United Kingdom, 1items

Citation

Journal: Acs Catalysis / Year: 2020
Title: Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms
Authors: Cuetos, A. / Iglesias-Fernandez, J. / Danesh-Azari, H.R. / Zukic, E. / Dowle, A. / Osuna, S. / Grogan, G.

History

Deposition	Nov 14, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 7, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6tfn.cif.gz	711.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6tfn.ent.gz	589 KB	Display	PDB format
PDBx/mmJSON format	6tfn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tf/6tfn ftp://data.pdbj.org/pub/pdb/validation_reports/tf/6tfn	HTTPS FTP

-
Related structure data

Related structure data	6t9hC 6tfrC 6tftC 6thmC 5g1uS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6t9h-1 6t9h-2 5hlr-d 5g1u-d 6tft-d 5i3t-d 5g1v-d 5g1w-d 6thm-d 5hss-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Linalool dehydratase-isomerase protein LDI

B: Linalool dehydratase-isomerase protein LDI

C: Linalool dehydratase-isomerase protein LDI

D: Linalool dehydratase-isomerase protein LDI

E: Linalool dehydratase-isomerase protein LDI

F: Linalool dehydratase-isomerase protein LDI

G: Linalool dehydratase-isomerase protein LDI

H: Linalool dehydratase-isomerase protein LDI

I: Linalool dehydratase-isomerase protein LDI

J: Linalool dehydratase-isomerase protein LDI

hetero molecules

421 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Linalool dehydratase-isomerase protein LDI

B: Linalool dehydratase-isomerase protein LDI

C: Linalool dehydratase-isomerase protein LDI

D: Linalool dehydratase-isomerase protein LDI

E: Linalool dehydratase-isomerase protein LDI

hetero molecules

defined by author&software
Evidence: gel filtration
210 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Linalool dehydratase-isomerase protein LDI

G: Linalool dehydratase-isomerase protein LDI

H: Linalool dehydratase-isomerase protein LDI

I: Linalool dehydratase-isomerase protein LDI

J: Linalool dehydratase-isomerase protein LDI

hetero molecules

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

Unit cell

Length a, b, c (Å)	87.775, 110.440, 236.485
Angle α, β, γ (deg.)	90.000, 99.200, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	A	A	4 - 365	4 - 365
2	1	LEU	LEU	B	B	4 - 365	4 - 365
1	2	LEU	LEU	A	A	4 - 365	4 - 365
2	2	LEU	LEU	C	C	4 - 365	4 - 365
1	3	PRO	PRO	A	A	5 - 364	5 - 364
2	3	PRO	PRO	D	D	5 - 364	5 - 364
1	4	LEU	LEU	A	A	4 - 364	4 - 364
2	4	LEU	LEU	E	E	4 - 364	4 - 364
1	5	PRO	PRO	A	A	5 - 364	5 - 364
2	5	PRO	PRO	F	F	5 - 364	5 - 364
1	6	LEU	LEU	A	A	4 - 364	4 - 364
2	6	LEU	LEU	G	G	4 - 364	4 - 364
1	7	LEU	LEU	A	A	4 - 364	4 - 364
2	7	LEU	LEU	H	H	4 - 364	4 - 364
1	8	LEU	LEU	A	A	4 - 364	4 - 364
2	8	LEU	LEU	I	I	4 - 364	4 - 364
1	9	LEU	LEU	A	A	4 - 364	4 - 364
2	9	LEU	LEU	J	J	4 - 364	4 - 364
1	10	LEU	LEU	B	B	4 - 365	4 - 365
2	10	LEU	LEU	C	C	4 - 365	4 - 365
1	11	PRO	PRO	B	B	5 - 364	5 - 364
2	11	PRO	PRO	D	D	5 - 364	5 - 364
1	12	LEU	LEU	B	B	4 - 364	4 - 364
2	12	LEU	LEU	E	E	4 - 364	4 - 364
1	13	PRO	PRO	B	B	5 - 364	5 - 364
2	13	PRO	PRO	F	F	5 - 364	5 - 364
1	14	LEU	LEU	B	B	4 - 364	4 - 364
2	14	LEU	LEU	G	G	4 - 364	4 - 364
1	15	LEU	LEU	B	B	4 - 364	4 - 364
2	15	LEU	LEU	H	H	4 - 364	4 - 364
1	16	LEU	LEU	B	B	4 - 364	4 - 364
2	16	LEU	LEU	I	I	4 - 364	4 - 364
1	17	LEU	LEU	B	B	4 - 364	4 - 364
2	17	LEU	LEU	J	J	4 - 364	4 - 364
1	18	PRO	PRO	C	C	5 - 364	5 - 364
2	18	PRO	PRO	D	D	5 - 364	5 - 364
1	19	LEU	LEU	C	C	4 - 364	4 - 364
2	19	LEU	LEU	E	E	4 - 364	4 - 364
1	20	PRO	PRO	C	C	5 - 364	5 - 364
2	20	PRO	PRO	F	F	5 - 364	5 - 364
1	21	LEU	LEU	C	C	4 - 364	4 - 364
2	21	LEU	LEU	G	G	4 - 364	4 - 364
1	22	LEU	LEU	C	C	4 - 364	4 - 364
2	22	LEU	LEU	H	H	4 - 364	4 - 364
1	23	LEU	LEU	C	C	4 - 364	4 - 364
2	23	LEU	LEU	I	I	4 - 364	4 - 364
1	24	LEU	LEU	C	C	4 - 364	4 - 364
2	24	LEU	LEU	J	J	4 - 364	4 - 364
1	25	PRO	PRO	D	D	5 - 364	5 - 364
2	25	PRO	PRO	E	E	5 - 364	5 - 364
1	26	PRO	PRO	D	D	5 - 365	5 - 365
2	26	PRO	PRO	F	F	5 - 365	5 - 365
1	27	PRO	PRO	D	D	5 - 364	5 - 364
2	27	PRO	PRO	G	G	5 - 364	5 - 364
1	28	PRO	PRO	D	D	5 - 364	5 - 364
2	28	PRO	PRO	H	H	5 - 364	5 - 364
1	29	PRO	PRO	D	D	5 - 364	5 - 364
2	29	PRO	PRO	I	I	5 - 364	5 - 364
1	30	PRO	PRO	D	D	5 - 364	5 - 364
2	30	PRO	PRO	J	J	5 - 364	5 - 364
1	31	PRO	PRO	E	E	5 - 364	5 - 364
2	31	PRO	PRO	F	F	5 - 364	5 - 364
1	32	ALA	ALA	E	E	2 - 365	2 - 365
2	32	ALA	ALA	G	G	2 - 365	2 - 365
1	33	GLU	GLU	E	E	3 - 364	3 - 364
2	33	GLU	GLU	H	H	3 - 364	3 - 364
1	34	GLU	GLU	E	E	3 - 364	3 - 364
2	34	GLU	GLU	I	I	3 - 364	3 - 364
1	35	ALA	ALA	E	E	2 - 365	2 - 365
2	35	ALA	ALA	J	J	2 - 365	2 - 365
1	36	PRO	PRO	F	F	5 - 364	5 - 364
2	36	PRO	PRO	G	G	5 - 364	5 - 364
1	37	PRO	PRO	F	F	5 - 364	5 - 364
2	37	PRO	PRO	H	H	5 - 364	5 - 364
1	38	PRO	PRO	F	F	5 - 364	5 - 364
2	38	PRO	PRO	I	I	5 - 364	5 - 364
1	39	PRO	PRO	F	F	5 - 364	5 - 364
2	39	PRO	PRO	J	J	5 - 364	5 - 364
1	40	GLU	GLU	G	G	3 - 364	3 - 364
2	40	GLU	GLU	H	H	3 - 364	3 - 364
1	41	GLU	GLU	G	G	3 - 364	3 - 364
2	41	GLU	GLU	I	I	3 - 364	3 - 364
1	42	ALA	ALA	G	G	2 - 365	2 - 365
2	42	ALA	ALA	J	J	2 - 365	2 - 365
1	43	GLU	GLU	H	H	3 - 365	3 - 365
2	43	GLU	GLU	I	I	3 - 365	3 - 365
1	44	GLU	GLU	H	H	3 - 364	3 - 364
2	44	GLU	GLU	J	J	3 - 364	3 - 364
1	45	GLU	GLU	I	I	3 - 364	3 - 364
2	45	GLU	GLU	J	J	3 - 364	3 - 364

NCS ensembles :

#1: Protein	Linalool dehydratase-isomerase protein LDI Mass: 41993.715 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Castellaniella defragrans 65Phen (bacteria) Gene: BN940_14136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8X534
#2: Chemical	ChemComp-N6Q / 7-methyl-3-methylidene-oct-1-ene Mass: 138.250 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₈ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.35 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.02 M phosphate buffer; 0.1 M bis-tris propane pH 6.5; 20% PEG 3350

-
Data collection

Diffraction	Mean temperature: 120 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection	Resolution: 2.18→49.97 Å / Num. obs: 228868 / % possible obs: 98.6 % / Redundancy: 4 % / CC_1/2: 1 / R_merge(I) obs: 0.1 / R_pim(I) all: 0.09 / Net I/σ(I): 7.3
Reflection shell	Resolution: 2.18→2.22 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 11471 / CC_1/2: 0.6 / R_pim(I) all: 0.58 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5G1U

5g1u

Resolution: 2.18→49.97 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.951 / SU B: 5.569 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.209	11483	5 %	RANDOM
R_work	0.1891	-	-	-
obs	0.1901	217357	98.57 %	-

Solvent computation

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

Displacement parameters

B_iso max: 136.48 Å² / B_iso mean: 35.172 Å² / B_iso min: 16.28 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.33 Å²	0 Å²	0.54 Å²
2-	-	-0.01 Å²	-0 Å²
3-	-	-	0.16 Å²

Refinement step

Cycle: final / Resolution: 2.18→49.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28609	0	60	965	29634
B_iso mean	-	-	64.54	34.45	-
Num. residues	-	-	-	-	3626

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	29570
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	26548
X-RAY DIFFRACTION	r_angle_refined_deg	1.428	1.642	40262
X-RAY DIFFRACTION	r_angle_other_deg	1.361	1.568	61280
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.421	5	3625
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.584	21.644	1539
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.762	15	4439
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.449	15	168
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	3709
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	33531
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6733

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	12274	0.03
1	2	B	12274	0.03
2	1	A	12316	0.04
2	2	C	12316	0.04
3	1	A	12221	0.04
3	2	D	12221	0.04
4	1	A	12285	0.04
4	2	E	12285	0.04
5	1	A	12308	0.03
5	2	F	12308	0.03
6	1	A	12286	0.04
6	2	G	12286	0.04
7	1	A	12280	0.04
7	2	H	12280	0.04
8	1	A	12303	0.04
8	2	I	12303	0.04
9	1	A	12279	0.04
9	2	J	12279	0.04
10	1	B	12342	0.03
10	2	C	12342	0.03
11	1	B	12243	0.03
11	2	D	12243	0.03
12	1	B	12311	0.03
12	2	E	12311	0.03
13	1	B	12311	0.03
13	2	F	12311	0.03
14	1	B	12321	0.03
14	2	G	12321	0.03
15	1	B	12299	0.03
15	2	H	12299	0.03
16	1	B	12330	0.03
16	2	I	12330	0.03
17	1	B	12303	0.03
17	2	J	12303	0.03
18	1	C	12288	0.04
18	2	D	12288	0.04
19	1	C	12378	0.03
19	2	E	12378	0.03
20	1	C	12353	0.04
20	2	F	12353	0.04
21	1	C	12373	0.03
21	2	G	12373	0.03
22	1	C	12402	0.03
22	2	H	12402	0.03
23	1	C	12396	0.03
23	2	I	12396	0.03
24	1	C	12372	0.03
24	2	J	12372	0.03
25	1	D	12342	0.04
25	2	E	12342	0.04
26	1	D	12377	0.04
26	2	F	12377	0.04
27	1	D	12310	0.04
27	2	G	12310	0.04
28	1	D	12332	0.04
28	2	H	12332	0.04
29	1	D	12362	0.03
29	2	I	12362	0.03
30	1	D	12322	0.04
30	2	J	12322	0.04
31	1	E	12347	0.03
31	2	F	12347	0.03
32	1	E	12409	0.04
32	2	G	12409	0.04
33	1	E	12438	0.03
33	2	H	12438	0.03
34	1	E	12417	0.04
34	2	I	12417	0.04
35	1	E	12513	0.02
35	2	J	12513	0.02
36	1	F	12337	0.03
36	2	G	12337	0.03
37	1	F	12348	0.03
37	2	H	12348	0.03
38	1	F	12370	0.03
38	2	I	12370	0.03
39	1	F	12338	0.03
39	2	J	12338	0.03
40	1	G	12372	0.04
40	2	H	12372	0.04
41	1	G	12402	0.04
41	2	I	12402	0.04
42	1	G	12415	0.04
42	2	J	12415	0.04
43	1	H	12538	0.04
43	2	I	12538	0.04
44	1	H	12485	0.03
44	2	J	12485	0.03
45	1	I	12447	0.04
45	2	J	12447	0.04

LS refinement shell

Resolution: 2.18→2.237 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.283	879	-
R_work	0.268	16221	-
all	-	17100	-
obs	-	-	99.85 %

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi