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- PDB-5i3t: Native Structure of the Linalool Dehydratase-Isomerase from Caste... -

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Basic information

Entry
Database: PDB / ID: 5i3t
TitleNative Structure of the Linalool Dehydratase-Isomerase from Castellaniella defragrans
ComponentsLinalool dehydratase/isomerase
KeywordsLYASE / ISOMERASE / linalool / dehydratase
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
1,3-BUTANEDIOL / : / Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCastellaniella defragrans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLaMattina, J.W. / Carlock, M. / Koch, D.J. / Lanzilotta, W.N.
CitationJournal: To Be Published
Title: Native Structure of the Linalool Dehydratase-Isomerase from Castellaniella defragrans
Authors: LaMattina, J.W. / Carlock, M. / Koch, D.J. / Lanzilotta, W.N.
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)223,16818
Polymers222,5285
Non-polymers63913
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14850 Å2
ΔGint-109 kcal/mol
Surface area59940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.957, 106.757, 188.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 44505.680 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Castellaniella defragrans (bacteria) / Gene: ldi / Production host: Escherichia coli (E. coli)
References: UniProt: E1XUJ2, linalool dehydratase, geraniol isomerase
#2: Chemical ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 8 / Details: 4-7% glycerol, 20-30% PEG 4000, 0.1 M TRIS pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→30.193 Å / Num. obs: 234053 / % possible obs: 99.7 % / Redundancy: 20 % / Net I/σ(I): 5.68

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.1→30.193 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 20.36
RfactorNum. reflection% reflection
Rfree0.2045 3824 1.63 %
Rwork0.1633 --
obs0.164 234053 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.37 Å2 / Biso mean: 33.2513 Å2 / Biso min: 18.27 Å2
Refinement stepCycle: final / Resolution: 2.1→30.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14480 0 28 519 15027
Biso mean--50.05 35.02 -
Num. residues----1811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814950
X-RAY DIFFRACTIONf_angle_d1.07820316
X-RAY DIFFRACTIONf_chiral_restr0.0422138
X-RAY DIFFRACTIONf_plane_restr0.0062628
X-RAY DIFFRACTIONf_dihedral_angle_d13.4565380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12660.3421280.27658394852298
2.1266-2.15460.33241340.2338496863099
2.1546-2.18410.26071510.22018535868699
2.1841-2.21530.2931480.215485068654100
2.2153-2.24830.2341510.206385428693100
2.2483-2.28340.2271560.194285058661100
2.2834-2.32080.28271040.187785348638100
2.3208-2.36090.23891640.179484828646100
2.3609-2.40380.25221350.179285178652100
2.4038-2.450.22051430.176385818724100
2.45-2.50.23011440.176585328676100
2.5-2.55430.22861260.173485558681100
2.5543-2.61370.21041550.171684918646100
2.6137-2.6790.22731340.176285098643100
2.679-2.75140.24341420.176485838725100
2.7514-2.83230.24181440.178285178661100
2.8323-2.92360.25591360.180985528688100
2.9236-3.0280.24191500.17985928742100
3.028-3.14920.22351240.193585618685100
3.1492-3.29230.20891390.18385338672100
3.2923-3.46570.2091460.174585188664100
3.4657-3.68240.21681360.165685728708100
3.6824-3.96620.17421440.14385208664100
3.9662-4.36430.13711540.121785468700100
4.3643-4.99330.15071480.118185208668100
4.9933-6.28170.17761400.140985488688100
6.2817-30.19660.14681480.12358488863699

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