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- PDB-5g1w: Apo Structure of Linalool Dehydratase-Isomerase -

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Basic information

Entry
Database: PDB / ID: 5g1w
TitleApo Structure of Linalool Dehydratase-Isomerase
ComponentsLINALOOL DEHYDRATASE/ISOMERASE
KeywordsLYASE / HYDRATASE / ISOMERASE / TERPENE / ALKENE
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
METHYLMALONIC ACID / Linalool dehydratase/isomerase
Similarity search - Component
Biological speciesCASTELLANIELLA DEFRAGRANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsChambers, S. / Hau, A. / Man, H. / Omar, M. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structural and functional insights into asymmetric enzymatic dehydration of alkenols.
Authors: Nestl, B.M. / Geinitz, C. / Popa, S. / Rizek, S. / Haselbeck, R.J. / Stephen, R. / Noble, M.A. / Fischer, M.P. / Ralph, E.C. / Hau, H.T. / Man, H. / Omar, M. / Turkenburg, J.P. / van Dien, S. ...Authors: Nestl, B.M. / Geinitz, C. / Popa, S. / Rizek, S. / Haselbeck, R.J. / Stephen, R. / Noble, M.A. / Fischer, M.P. / Ralph, E.C. / Hau, H.T. / Man, H. / Omar, M. / Turkenburg, J.P. / van Dien, S. / Culler, S.J. / Grogan, G. / Hauer, B.
History
DepositionMar 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 2.0Nov 9, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / struct_ncs_oper / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[3][3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.3Nov 6, 2024Group: Structure summary / Category: pdbx_contact_author

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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)210,88718
Polymers209,9695
Non-polymers91913
Water37,7232094
1
A: LINALOOL DEHYDRATASE/ISOMERASE
B: LINALOOL DEHYDRATASE/ISOMERASE
C: LINALOOL DEHYDRATASE/ISOMERASE
D: LINALOOL DEHYDRATASE/ISOMERASE
E: LINALOOL DEHYDRATASE/ISOMERASE
hetero molecules

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)421,77536
Polymers419,93710
Non-polymers1,83826
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area31650 Å2
ΔGint-26.3 kcal/mol
Surface area117380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.062, 110.148, 195.338
Angle α, β, γ (deg.)90.00, 91.32, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-1370-

DXX

21A-2187-

HOH

31A-2265-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, -0.00344), (0.3273, -0.9449, 0.00151), (0.9449, 0.3273)-0.1501, -62.24, 87.29
2given(-0.002713, -0.004572), (-0.8181, -0.575, -0.000103), (0.575, -0.8181)-0.5062, -166.7, 51.65
3given(1, 0.002524, 0.001325), (-0.002051, 0.3144, 0.9493), (0.001979, -0.9493, 0.3144)0.1613, -63.2, -87.12
4given(0.9999, -0.003135, 0.0103), (-0.008451, -0.8214, 0.5703), (0.006674, -0.5704, -0.8214)-0.5929, -167, -51.2

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Components

#1: Protein
LINALOOL DEHYDRATASE/ISOMERASE / GERANIOL ISOMERASE / LINALOOL DEHYDRATASE-ISOMERASE / MYRCENE HYDRATASE / LINALOOL DEHYDRATASE ISOMERASE


Mass: 41993.715 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CASTELLANIELLA DEFRAGRANS (bacteria) / Strain: 65PHEN / Plasmid: PET-YSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E1XUJ2, linalool dehydratase, geraniol isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DXX / METHYLMALONIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2094 / 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: 2.77 Å3/Da / Density % sol: 55.6 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M BIS-TRIS PROPANE BUFFER PH 6.5 WITH 25% (W/V) PEG 3350, 10% (W/V) METHYLPENTANE DIOL AND 0.1 M SODIUM MALONATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorDate: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.76→47.97 Å / Num. obs: 218882 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.6
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.7 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEMET STRUCTURE

Resolution: 1.76→47.97 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.242 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 10822 4.9 %RANDOM
Rwork0.1505 ---
obs0.15178 208055 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å20.14 Å2
2--1.32 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.76→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14429 0 58 2094 16581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01914927
X-RAY DIFFRACTIONr_bond_other_d0.0110.0213724
X-RAY DIFFRACTIONr_angle_refined_deg1.821.95220307
X-RAY DIFFRACTIONr_angle_other_deg1.602331534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05351827
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44123.281695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.092152276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2291586
X-RAY DIFFRACTIONr_chiral_restr0.120.22147
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02116971
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023591
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7261.7797295
X-RAY DIFFRACTIONr_mcbond_other1.7261.7797296
X-RAY DIFFRACTIONr_mcangle_it2.2692.6589111
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1082.0887629
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 835 -
Rwork0.27 15120 -
obs--95.87 %

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