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- PDB-5vgs: Crystal structure of lachrymatory factor synthase from Allium cep... -

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Basic information

Entry
Database: PDB / ID: 5vgs
TitleCrystal structure of lachrymatory factor synthase from Allium cepa in complex with crotyl alcohol
ComponentsLachrymatory-factor synthase
KeywordsISOMERASE / lachrymatory factor / onion / sulfenic acid / crotyl alcohol
Function / homology
Function and homology information


lachrymatory-factor synthase / vacuole / isomerase activity
Similarity search - Function
: / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START-like domain superfamily
Similarity search - Domain/homology
(2Z)-but-2-en-1-ol / (2E)-but-2-en-1-ol / Lachrymatory-factor synthase
Similarity search - Component
Biological speciesAllium cepa (onion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSilvaroli, J.A. / Pleshinger, M.J. / Banerjee, S. / Kiser, P.D. / Golczak, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Enzyme That Makes You Cry-Crystal Structure of Lachrymatory Factor Synthase from Allium cepa.
Authors: Silvaroli, J.A. / Pleshinger, M.J. / Banerjee, S. / Kiser, P.D. / Golczak, M.
History
DepositionApr 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7223
Polymers17,5781
Non-polymers1442
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.930, 40.100, 97.630
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: 17577.947 Da / Num. of mol.: 1
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-9A4 / (2Z)-but-2-en-1-ol


Mass: 72.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O
#3: Chemical ChemComp-9A7 / (2E)-but-2-en-1-ol


Mass: 72.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.17 Å3/Da / Density % sol: 43.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5 containing PEG 3350 at concentrations between 25%-32% (w/v)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→40.1 Å / Num. obs: 12549 / % possible obs: 99.4 % / Redundancy: 5.2 % / Rsym value: 0.0153 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 761 / CC1/2: 0.66 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VGL

5vgl


Resolution: 1.9→37.093 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 628 5.02 %
Rwork0.1668 --
obs0.1693 12510 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→37.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 10 202 1422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091258
X-RAY DIFFRACTIONf_angle_d0.9941698
X-RAY DIFFRACTIONf_dihedral_angle_d16.516739
X-RAY DIFFRACTIONf_chiral_restr0.054181
X-RAY DIFFRACTIONf_plane_restr0.006217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.09120.28061640.21442835X-RAY DIFFRACTION97
2.0912-2.39380.22911430.16882963X-RAY DIFFRACTION100
2.3938-3.01570.20391610.17082978X-RAY DIFFRACTION100
3.0157-37.10.19791600.15113106X-RAY DIFFRACTION99

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