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- PDB-6ies: Onion lachrymatory factor synthase (LFS) containing (E)-2-propen ... -

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Basic information

Entry
Database: PDB / ID: 6ies
TitleOnion lachrymatory factor synthase (LFS) containing (E)-2-propen 1-ol (crotyl alcohol)
ComponentsLachrymatory-factor synthase
KeywordsISOMERASE / SRPBCC / helix-grip fold / cytosolic
Function / homologylachrymatory-factor synthase / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / vacuole / START-like domain superfamily / (2E)-but-2-en-1-ol / Lachrymatory-factor synthase
Function and homology information
Biological speciesAllium cepa (onion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSato, Y. / Arakawa, T. / Takabe, J. / Masamura, N. / Tsuge, N. / Imai, S. / Fushinobu, S.
CitationJournal: Acs Catalysis / Year: 2020
Title: Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase.
Authors: Arakawa, T. / Sato, Y. / Yamada, M. / Takabe, J. / Yoshitaka Moriwaki, Y. / Masamura, N. / Kato, M. / Aoyagi, M. / Kamoi, T. / Terada, T. / Shimizu, K. / Tsuge, N. / Imai, S. / Fushinobu, S.
History
DepositionSep 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lachrymatory-factor synthase
B: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9554
Polymers39,8112
Non-polymers1442
Water2,900161
1
A: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9782
Polymers19,9061
Non-polymers721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9782
Polymers19,9061
Non-polymers721
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.090, 50.090, 141.397
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Lachrymatory-factor synthase


Mass: 19905.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allium cepa (onion) / Gene: LFS / Production host: Escherichia coli (E. coli) / References: UniProt: P59082
#2: Chemical ChemComp-9A7 / (2E)-but-2-en-1-ol


Mass: 72.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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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: 2.23 Å3/Da / Density % sol: 44.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG6000, 0.1 M MES-Na

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 32193 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 28.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.53 / Num. unique obs: 1565 / CC1/2: 0.9 / Rsym value: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GTE

5gte


Resolution: 1.8→31.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.511 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 1559 4.9 %RANDOM
Rwork0.1787 ---
obs0.18 30579 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.87 Å2 / Biso mean: 28.869 Å2 / Biso min: 16.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 10 161 2601
Biso mean--31.11 32.37 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0152502
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172246
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.7293380
X-RAY DIFFRACTIONr_angle_other_deg0.5631.7225254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14922.43982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62315366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.198154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
LS refinement shellResolution: 1.799→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 110 -
Rwork0.223 2233 -
all-2343 -
obs--98.82 %

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