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- PDB-7ad2: Linalool Dehydratase Isomerase G107T mutant -

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Basic information

Entry
Database: PDB / ID: 7ad2
TitleLinalool Dehydratase Isomerase G107T mutant
ComponentsLinalool dehydratase/isomerase
KeywordsLYASE / Linalool / dehydratase / isomerase / 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
Linalool dehydratase/isomerase / Linalool dehydratase/isomerase
Similarity search - Domain/homology
MALONATE ION / Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCastellaniella defragrans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsCuetos, A. / Fischer, M.P. / Hauer, B. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P005578/1 United Kingdom
CitationJournal: To Be Published
Title: Linalool Dehydratase Isomerase G107T mutant
Authors: Cuetos, A. / Fischer, M.P. / Hauer, B. / Grogan, G.
History
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id ..._diffrn_source.pdbx_synchrotron_site / _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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Linalool dehydratase/isomerase
B: Linalool dehydratase/isomerase
C: Linalool dehydratase/isomerase
D: Linalool dehydratase/isomerase
E: Linalool dehydratase/isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,3937
Polymers210,1895
Non-polymers2042
Water27,2391512
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-59 kcal/mol
Surface area61140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.984, 110.763, 108.590
Angle α, β, γ (deg.)90.000, 117.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-666-

HOH

21A-691-

HOH

31A-715-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:

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

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA2 - 3652 - 365
21ALAALABB2 - 3652 - 365
12ALAALAAA2 - 3642 - 364
22ALAALACC2 - 3642 - 364
13ALAALAAA2 - 3642 - 364
23ALAALADD2 - 3642 - 364
14ALAALAAA2 - 3642 - 364
24ALAALAEE2 - 3642 - 364
15ALAALABB2 - 3642 - 364
25ALAALACC2 - 3642 - 364
16ALAALABB2 - 3642 - 364
26ALAALADD2 - 3642 - 364
17ALAALABB2 - 3642 - 364
27ALAALAEE2 - 3642 - 364
18ALAALACC2 - 3642 - 364
28ALAALADD2 - 3642 - 364
19METMETCC1 - 3651 - 365
29METMETEE1 - 3651 - 365
110ALAALADD2 - 3642 - 364
210ALAALAEE2 - 3642 - 364

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Linalool dehydratase/isomerase / Geraniol isomerase / Linalool dehydratase-isomerase / Myrcene hydratase


Mass: 42037.770 Da / Num. of mol.: 5 / Mutation: G107T
Source method: isolated from a genetically manipulated source
Details: G107T mutant / 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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 5 mg mL-1 protein concentration, 0.2 M sodium malonate, 0.1 M Bis-Tris propane pH 6.0, 20% w/w PEG 3350 and 3% (v/v) methyl-2,4-pentanediol (MPD).

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.83→98.04 Å / Num. obs: 198119 / % possible obs: 93.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 12 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.1 / Net I/σ(I): 6.5
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 14473 / CC1/2: 0.54 / Rpim(I) all: 0.49 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1U

5g1u


Resolution: 1.83→98.02 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.086 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2399 9850 5 %RANDOM
Rwork0.2138 ---
obs0.2151 186754 96.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.65 Å2 / Biso mean: 16.25 Å2 / Biso min: 6.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å2-0.31 Å2
2--2.46 Å20 Å2
3----1.55 Å2
Refinement stepCycle: final / Resolution: 1.83→98.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14497 0 14 1512 16023
Biso mean--18.88 25.53 -
Num. residues----1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01314944
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713395
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.64220347
X-RAY DIFFRACTIONr_angle_other_deg1.3891.56830954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3751819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13421.673801
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.192152282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2151593
X-RAY DIFFRACTIONr_chiral_restr0.080.21874
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023399
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A126580.04
12B126580.04
21A126490.04
22C126490.04
31A126620.04
32D126620.04
41A126750.03
42E126750.03
51B126700.04
52C126700.04
61B126850.03
62D126850.03
71B126260.04
72E126260.04
81C126630.04
82D126630.04
91C127300.04
92E127300.04
101D126380.04
102E126380.04
LS refinement shellResolution: 1.83→1.877 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.394 728 -
Rwork0.386 13254 -
obs--92.74 %

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