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- PDB-6thm: Linalool Dehydratase Isomerase M125A mutant -

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Basic information

Entry
Database: PDB / ID: 6thm
TitleLinalool Dehydratase Isomerase M125A 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
MALONATE ION / Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCastellaniella defragrans 65Phen (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,80322
Polymers209,6685
Non-polymers1,13517
Water14,844824
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14210 Å2
ΔGint-23 kcal/mol
Surface area61360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.670, 110.689, 196.715
Angle α, β, γ (deg.)90.000, 91.260, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

21A-644-

HOH

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Components

#1: Protein
Linalool dehydratase-isomerase protein LDI


Mass: 41933.598 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: M125A mutant
Source: (gene. exp.) Castellaniella defragrans 65Phen (bacteria)
Gene: BN940_14136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8X534
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MLI / MALONATE ION


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


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium malonate; 0.1 M bis-tris propane pH 7.5; 20% (w/w) PEG3350; 5% (v/v) methylpentanediol

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.99→98.33 Å / Num. obs: 156439 / % possible obs: 98.4 % / Redundancy: 4.2 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 1.99→2.02 Å / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 7677 / CC1/2: 0.68 / Rpim(I) all: 0.77

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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: 1.99→96.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.662 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.141
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 7886 5 %RANDOM
Rwork0.178 ---
obs0.1799 148547 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.42 Å2 / Biso mean: 33.191 Å2 / Biso min: 21.02 Å2
Baniso -1Baniso -2Baniso -3
1--3.1 Å20 Å20.13 Å2
2--2.37 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.99→96.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14416 0 74 824 15314
Biso mean--56.99 39.26 -
Num. residues----1825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01314932
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713437
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.64420296
X-RAY DIFFRACTIONr_angle_other_deg1.3921.56731023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73551824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28421.536781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.988152248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3151594
X-RAY DIFFRACTIONr_chiral_restr0.0830.21865
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023397
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 543 -
Rwork0.302 10930 -
all-11473 -
obs--97.37 %

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