PDB-6t9h: C171S mutant of Linalool Dehydratase Isomerase

ID or keywords:

Entry

Database: PDB / ID: 6t9h

Title

C171S mutant of Linalool Dehydratase Isomerase

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 / cellular response to organic substance / protein tetramerization /

periplasmic space
Similarity search - Function

Biological species

Castellaniella defragrans 65Phen (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.58 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	Oct 28, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6t9h.cif.gz	704.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6t9h.ent.gz	583.8 KB	Display	PDB format
PDBx/mmJSON format	6t9h.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/t9/6t9h ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t9h	HTTPS FTP

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Related structure data

Related structure data	6tfnC 6tfrC 6tftC 6thmC 5g1wS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6tfn-2 6tfn-1 5i3t-d 5hlr-d 5g1u-d 5g1v-d 6thm-d 6tft-d 5g1w-d 6tfr-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

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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

S: Linalool dehydratase-isomerase protein LDI

T: Linalool dehydratase-isomerase protein LDI

U: Linalool dehydratase-isomerase protein LDI

V: Linalool dehydratase-isomerase protein LDI

W: Linalool dehydratase-isomerase protein LDI

420 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

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

2

S: Linalool dehydratase-isomerase protein LDI

T: Linalool dehydratase-isomerase protein LDI

U: Linalool dehydratase-isomerase protein LDI

V: Linalool dehydratase-isomerase protein LDI

W: Linalool dehydratase-isomerase protein LDI

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

Unit cell

Length a, b, c (Å)	87.774, 109.469, 232.782
Angle α, β, γ (deg.)	90.000, 99.530, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0

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	GLU	GLU	A	A	3 - 365	3 - 365
2	1	GLU	GLU	B	B	3 - 365	3 - 365
1	2	GLU	GLU	A	A	3 - 365	3 - 365
2	2	GLU	GLU	C	C	3 - 365	3 - 365
1	3	GLU	GLU	A	A	3 - 365	3 - 365
2	3	GLU	GLU	D	D	3 - 365	3 - 365
1	4	LEU	LEU	A	A	4 - 364	4 - 364
2	4	LEU	LEU	E	E	4 - 364	4 - 364
1	5	GLU	GLU	A	A	3 - 365	3 - 365
2	5	GLU	GLU	S	F	3 - 365	3 - 365
1	6	LEU	LEU	A	A	4 - 364	4 - 364
2	6	LEU	LEU	T	G	4 - 364	4 - 364
1	7	LEU	LEU	A	A	4 - 364	4 - 364
2	7	LEU	LEU	U	H	4 - 364	4 - 364
1	8	PRO	PRO	A	A	5 - 364	5 - 364
2	8	PRO	PRO	V	I	5 - 364	5 - 364
1	9	LEU	LEU	A	A	4 - 364	4 - 364
2	9	LEU	LEU	W	J	4 - 364	4 - 364
1	10	GLU	GLU	B	B	3 - 365	3 - 365
2	10	GLU	GLU	C	C	3 - 365	3 - 365
1	11	GLU	GLU	B	B	3 - 365	3 - 365
2	11	GLU	GLU	D	D	3 - 365	3 - 365
1	12	LEU	LEU	B	B	4 - 364	4 - 364
2	12	LEU	LEU	E	E	4 - 364	4 - 364
1	13	GLU	GLU	B	B	3 - 365	3 - 365
2	13	GLU	GLU	S	F	3 - 365	3 - 365
1	14	LEU	LEU	B	B	4 - 364	4 - 364
2	14	LEU	LEU	T	G	4 - 364	4 - 364
1	15	LEU	LEU	B	B	4 - 364	4 - 364
2	15	LEU	LEU	U	H	4 - 364	4 - 364
1	16	PRO	PRO	B	B	5 - 364	5 - 364
2	16	PRO	PRO	V	I	5 - 364	5 - 364
1	17	LEU	LEU	B	B	4 - 364	4 - 364
2	17	LEU	LEU	W	J	4 - 364	4 - 364
1	18	GLU	GLU	C	C	3 - 365	3 - 365
2	18	GLU	GLU	D	D	3 - 365	3 - 365
1	19	LEU	LEU	C	C	4 - 364	4 - 364
2	19	LEU	LEU	E	E	4 - 364	4 - 364
1	20	GLU	GLU	C	C	3 - 365	3 - 365
2	20	GLU	GLU	S	F	3 - 365	3 - 365
1	21	LEU	LEU	C	C	4 - 364	4 - 364
2	21	LEU	LEU	T	G	4 - 364	4 - 364
1	22	LEU	LEU	C	C	4 - 364	4 - 364
2	22	LEU	LEU	U	H	4 - 364	4 - 364
1	23	PRO	PRO	C	C	5 - 364	5 - 364
2	23	PRO	PRO	V	I	5 - 364	5 - 364
1	24	LEU	LEU	C	C	4 - 364	4 - 364
2	24	LEU	LEU	W	J	4 - 364	4 - 364
1	25	LEU	LEU	D	D	4 - 364	4 - 364
2	25	LEU	LEU	E	E	4 - 364	4 - 364
1	26	GLU	GLU	D	D	3 - 365	3 - 365
2	26	GLU	GLU	S	F	3 - 365	3 - 365
1	27	LEU	LEU	D	D	4 - 364	4 - 364
2	27	LEU	LEU	T	G	4 - 364	4 - 364
1	28	LEU	LEU	D	D	4 - 364	4 - 364
2	28	LEU	LEU	U	H	4 - 364	4 - 364
1	29	PRO	PRO	D	D	5 - 364	5 - 364
2	29	PRO	PRO	V	I	5 - 364	5 - 364
1	30	LEU	LEU	D	D	4 - 364	4 - 364
2	30	LEU	LEU	W	J	4 - 364	4 - 364
1	31	LEU	LEU	E	E	4 - 364	4 - 364
2	31	LEU	LEU	S	F	4 - 364	4 - 364
1	32	LEU	LEU	E	E	4 - 365	4 - 365
2	32	LEU	LEU	T	G	4 - 365	4 - 365
1	33	LEU	LEU	E	E	4 - 365	4 - 365
2	33	LEU	LEU	U	H	4 - 365	4 - 365
1	34	PRO	PRO	E	E	5 - 364	5 - 364
2	34	PRO	PRO	V	I	5 - 364	5 - 364
1	35	LEU	LEU	E	E	4 - 365	4 - 365
2	35	LEU	LEU	W	J	4 - 365	4 - 365
1	36	LEU	LEU	S	F	4 - 364	4 - 364
2	36	LEU	LEU	T	G	4 - 364	4 - 364
1	37	LEU	LEU	S	F	4 - 364	4 - 364
2	37	LEU	LEU	U	H	4 - 364	4 - 364
1	38	PRO	PRO	S	F	5 - 364	5 - 364
2	38	PRO	PRO	V	I	5 - 364	5 - 364
1	39	LEU	LEU	S	F	4 - 364	4 - 364
2	39	LEU	LEU	W	J	4 - 364	4 - 364
1	40	LEU	LEU	T	G	4 - 365	4 - 365
2	40	LEU	LEU	U	H	4 - 365	4 - 365
1	41	PRO	PRO	T	G	5 - 364	5 - 364
2	41	PRO	PRO	V	I	5 - 364	5 - 364
1	42	LEU	LEU	T	G	4 - 365	4 - 365
2	42	LEU	LEU	W	J	4 - 365	4 - 365
1	43	PRO	PRO	U	H	5 - 364	5 - 364
2	43	PRO	PRO	V	I	5 - 364	5 - 364
1	44	LEU	LEU	U	H	4 - 365	4 - 365
2	44	LEU	LEU	W	J	4 - 365	4 - 365
1	45	PRO	PRO	V	I	5 - 364	5 - 364
2	45	PRO	PRO	W	J	5 - 364	5 - 364

NCS ensembles :

#1: Protein	Linalool dehydratase-isomerase protein LDI Mass: 41977.652 Da / Num. of mol.: 10 / Mutation: C171S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Castellaniella defragrans 65Phen (bacteria) Gene: BN940_14136 / Plasmid: pET-YSBL-LIC / Production host: Escherichia coli (E. coli) / References: UniProt: W8X534
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 876 / 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: 2.63 Å³/Da / Density % sol: 53.19 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.02 M potassium phosphate; 0.1 M bis-tris propoane; 20% w/v PEG 3350; 10 mM linalool.

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Jul 31, 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: 2.58→76.52 Å / Num. obs: 135904 / % possible obs: 99.3 % / Redundancy: 4.1 % / CC_1/2: 1 / R_merge(I) obs: 0.11 / R_pim(I) all: 0.09 / Net I/σ(I): 8.7
Reflection shell	Resolution: 2.58→2.62 Å / R_merge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6447 / CC_1/2: 0.64 / R_pim(I) all: 0.64

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5G1W

5g1w

Resolution: 2.58→67.99 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.937 / SU B: 10.645 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.746 / ESU R Free: 0.265
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2117	6674	4.9 %	RANDOM
R_work	0.1794	-	-	-
obs	0.181	129181	99.25 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 135.55 Å² / B_iso mean: 41.213 Å² / B_iso min: 14.59 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.59 Å²	-0 Å²	1.81 Å²
2-	-	-1.27 Å²	-0 Å²
3-	-	-	2.13 Å²

Refinement step

Cycle: final / Resolution: 2.58→67.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28482	0	0	876	29358
B_iso mean	-	-	-	37.29	-
Num. residues	-	-	-	-	3624

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	29350
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	26251
X-RAY DIFFRACTION	r_angle_refined_deg	1.469	1.641	40008
X-RAY DIFFRACTION	r_angle_other_deg	1.344	1.569	60574
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.376	5	3614
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.14	21.651	1514
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.412	15	4350
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.984	15	169
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	3704
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	33301
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	6686

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	12224	0.04
1	2	B	12224	0.04
2	1	A	12229	0.04
2	2	C	12229	0.04
3	1	A	12236	0.04
3	2	D	12236	0.04
4	1	A	12214	0.04
4	2	E	12214	0.04
5	1	A	12315	0.03
5	2	S	12315	0.03
6	1	A	12130	0.04
6	2	T	12130	0.04
7	1	A	12030	0.03
7	2	U	12030	0.03
8	1	A	12135	0.04
8	2	V	12135	0.04
9	1	A	12216	0.04
9	2	W	12216	0.04
10	1	B	12188	0.04
10	2	C	12188	0.04
11	1	B	12260	0.04
11	2	D	12260	0.04
12	1	B	12182	0.04
12	2	E	12182	0.04
13	1	B	12200	0.05
13	2	S	12200	0.05
14	1	B	12117	0.04
14	2	T	12117	0.04
15	1	B	12054	0.04
15	2	U	12054	0.04
16	1	B	12152	0.03
16	2	V	12152	0.03
17	1	B	12201	0.05
17	2	W	12201	0.05
18	1	C	12271	0.03
18	2	D	12271	0.03
19	1	C	12193	0.03
19	2	E	12193	0.03
20	1	C	12266	0.04
20	2	S	12266	0.04
21	1	C	12149	0.04
21	2	T	12149	0.04
22	1	C	12061	0.04
22	2	U	12061	0.04
23	1	C	12179	0.02
23	2	V	12179	0.02
24	1	C	12171	0.04
24	2	W	12171	0.04
25	1	D	12277	0.04
25	2	E	12277	0.04
26	1	D	12265	0.04
26	2	S	12265	0.04
27	1	D	12175	0.04
27	2	T	12175	0.04
28	1	D	12045	0.04
28	2	U	12045	0.04
29	1	D	12261	0.03
29	2	V	12261	0.03
30	1	D	12234	0.05
30	2	W	12234	0.05
31	1	E	12213	0.04
31	2	S	12213	0.04
32	1	E	12189	0.04
32	2	T	12189	0.04
33	1	E	12083	0.03
33	2	U	12083	0.03
34	1	E	12185	0.03
34	2	V	12185	0.03
35	1	E	12291	0.04
35	2	W	12291	0.04
36	1	S	12161	0.04
36	2	T	12161	0.04
37	1	S	12066	0.03
37	2	U	12066	0.03
38	1	S	12176	0.04
38	2	V	12176	0.04
39	1	S	12232	0.04
39	2	W	12232	0.04
40	1	T	12073	0.03
40	2	U	12073	0.03
41	1	T	12111	0.04
41	2	V	12111	0.04
42	1	T	12185	0.04
42	2	W	12185	0.04
43	1	U	12015	0.04
43	2	V	12015	0.04
44	1	U	12129	0.03
44	2	W	12129	0.03
45	1	V	12170	0.04
45	2	W	12170	0.04

LS refinement shell

Resolution: 2.58→2.647 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.318	437	-
R_work	0.291	9326	-
all	-	9763	-
obs	-	-	96.58 %

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