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- PDB-5gtf: Crystal structure of onion lachrymatory factor synthase (LFS) con... -

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Basic information

Entry
Database: PDB / ID: 5gtf
TitleCrystal structure of onion lachrymatory factor synthase (LFS) containing glycerol
ComponentsLachrymatory-factor synthase
KeywordsISOMERASE / SRPBCC / helix-grip fold / cytosolic
Function / homologyPolyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / vacuole / START-like domain superfamily / Lachrymatory-factor synthase
Function and homology information
Biological speciesAllium cepa (onion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTakabe, J. / Arakawa, T. / 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. / Moriwaki, Y. / Masamura, N. / Kato, M. / Aoyagi, M. / Kamoi, T. / Terada, T. / Shimizu, K. / Tsuge, N. / Imai, S. / Fushinobu, S.
History
DepositionAug 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: 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 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: Lachrymatory-factor synthase
D: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,03518
Polymers79,6224
Non-polymers1,41214
Water11,674648
1
A: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1864
Polymers19,9061
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-15 kcal/mol
Surface area7500 Å2
MethodPISA
2
B: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3746
Polymers19,9061
Non-polymers4685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area7300 Å2
MethodPISA
3
C: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2825
Polymers19,9061
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area7960 Å2
MethodPISA
4
D: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1933
Polymers19,9061
Non-polymers2872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.000, 119.935, 125.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Lachrymatory-factor synthase


Mass: 19905.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Allium cepa (onion) / Gene: LFS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI
References: UniProt: P59082, Isomerases; Intramolecular oxidoreductases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, MES / PH range: 6.0 -6.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, direct water cooling using micro- channel (1st crystal), indirect water cooling (2nd crystal)
Protocol: 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: 91533 / % possible obs: 99.7 % / Redundancy: 5.8 % / Net I/σ(I): 18.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.2 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMET-derivatized model of identical protein

Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.216 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19854 4585 5 %RANDOM
Rwork0.16989 ---
obs0.17132 86948 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.514 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 85 648 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195098
X-RAY DIFFRACTIONr_bond_other_d0.0010.024713
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9456889
X-RAY DIFFRACTIONr_angle_other_deg0.89310933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.31925.172232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5715891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1231510
X-RAY DIFFRACTIONr_chiral_restr0.1240.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025597
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021141
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_it1.7841.7822422
X-RAY DIFFRACTIONr_mcbond_other1.7661.7812421
X-RAY DIFFRACTIONr_mcangle_it2.4752.6573023
X-RAY DIFFRACTIONr_mcangle_other2.4752.6593024
X-RAY DIFFRACTIONr_scbond_it3.362.2172676
X-RAY DIFFRACTIONr_scbond_other3.362.2172676
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1053.1593862
X-RAY DIFFRACTIONr_long_range_B_refined9.6117.2046568
X-RAY DIFFRACTIONr_long_range_B_other9.23416.3126209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.798→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 330 -
Rwork0.272 6196 -
obs--97.1 %

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