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- PDB-6tft: Linalool Dehydratase Isomerase C171A mutant -

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Basic information

Entry
Database: PDB / ID: 6tft
TitleLinalool Dehydratase Isomerase C171A mutant
ComponentsLinalool dehydratase-isomerase protein LDI
KeywordsLYASE / 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
Linalool dehydratase/isomerase / Linalool dehydratase/isomerase
Similarity search - Domain/homology
Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCastellaniella defragrans 65Phen (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsCuetos, A. / Zukic, E. / Danesh-Azari, H.R. / Grogan, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P005578/1 United Kingdom
CitationJournal: 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
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)209,8085
Polymers209,8085
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-59 kcal/mol
Surface area62440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.606, 111.814, 120.934
Angle α, β, γ (deg.)90.000, 102.240, 90.000
Int Tables number4
Space group name H-MP1211
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
11GLUGLUAA3 - 3643 - 364
21GLUGLUBB3 - 3643 - 364
12GLUGLUAA3 - 3653 - 365
22GLUGLUCC3 - 3653 - 365
13LEULEUAA4 - 3654 - 365
23LEULEUDD4 - 3654 - 365
14PROPROAA5 - 3645 - 364
24PROPROEE5 - 3645 - 364
15GLUGLUBB3 - 3643 - 364
25GLUGLUCC3 - 3643 - 364
16LEULEUBB4 - 3644 - 364
26LEULEUDD4 - 3644 - 364
17PROPROBB5 - 3645 - 364
27PROPROEE5 - 3645 - 364
18LEULEUCC4 - 3654 - 365
28LEULEUDD4 - 3654 - 365
19PROPROCC5 - 3645 - 364
29PROPROEE5 - 3645 - 364
110PROPRODD5 - 3645 - 364
210PROPROEE5 - 3645 - 364

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

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Components

#1: Protein
Linalool dehydratase-isomerase protein LDI


Mass: 41961.652 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: C171A mutant
Source: (gene. exp.) Castellaniella defragrans 65Phen (bacteria)
Gene: BN940_14136 / Production host: Escherichia coli (E. coli) / References: UniProt: W8X534
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: bis-Tris propane pH 5.5; 25% PEG 2000MME; 0.2 M potassium bromide

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.52→87.72 Å / Num. obs: 78481 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.09 / Net I/σ(I): 6.7
Reflection shellResolution: 2.52→2.57 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4473 / CC1/2: 0.65 / Rpim(I) all: 0.66

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1U

5g1u


Resolution: 2.52→87.72 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.621 / SU ML: 0.287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.524 / ESU R Free: 0.287
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 3898 5 %RANDOM
Rwork0.219 ---
obs0.2207 74562 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.66 Å2 / Biso mean: 49.66 Å2 / Biso min: 15.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.84 Å2-0 Å2-1.38 Å2
2--3.28 Å20 Å2
3---1.06 Å2
Refinement stepCycle: final / Resolution: 2.52→87.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14270 0 0 190 14460
Biso mean---38.46 -
Num. residues----1817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01314722
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713152
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.64120071
X-RAY DIFFRACTIONr_angle_other_deg1.2831.56830343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.50651816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68521.658766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.034152176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.11586
X-RAY DIFFRACTIONr_chiral_restr0.0710.21858
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023360
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A119380.05
12B119380.05
21A119670.05
22C119670.05
31A117200.06
32D117200.06
41A114470.05
42E114470.05
51B119080.04
52C119080.04
61B117060.05
62D117060.05
71B114090.05
72E114090.05
81C117000.06
82D117000.06
91C114760.05
92E114760.05
101D113890.05
102E113890.05
LS refinement shellResolution: 2.52→2.585 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 283 -
Rwork0.362 5493 -
all-5776 -
obs--99.76 %

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