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- PDB-5vgl: Crystal structure of lachrymatory factor synthase from Allium cepa -

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Basic information

Entry
Database: PDB / ID: 5vgl
TitleCrystal structure of lachrymatory factor synthase from Allium cepa
ComponentsLachrymatory-factor synthase
KeywordsISOMERASE / lachrymatory factor / onion / sulfenic acid
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: 1.4 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


Theoretical massNumber of molelcules
Total (without water)17,5781
Polymers17,5781
Non-polymers00
Water4,954275
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)39.072, 40.127, 98.514
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.2 Å3/Da / Density % sol: 44.01 %
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-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.4→40.13 Å / Num. obs: 34456 / % possible obs: 97.8 % / Redundancy: 4.1 % / CC1/2: 0.995 / Rsym value: 0.112 / Net I/σ(I): 8.4
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9045 / CC1/2: 0.62 / Rsym value: 0.789 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F08

3f08


Resolution: 1.4→37.162 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 1523 4.95 %
Rwork0.1519 --
obs0.1537 30780 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→37.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 0 275 1492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081355
X-RAY DIFFRACTIONf_angle_d0.9381848
X-RAY DIFFRACTIONf_dihedral_angle_d20.725516
X-RAY DIFFRACTIONf_chiral_restr0.078195
X-RAY DIFFRACTIONf_plane_restr0.006239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4001-1.44530.28631560.21832537X-RAY DIFFRACTION96
1.4453-1.49690.28041460.18532583X-RAY DIFFRACTION98
1.4969-1.55690.23021290.16512620X-RAY DIFFRACTION98
1.5569-1.62770.20861190.15322613X-RAY DIFFRACTION98
1.6277-1.71350.18991440.13142640X-RAY DIFFRACTION99
1.7135-1.82090.17611570.13212645X-RAY DIFFRACTION99
1.8209-1.96150.16971220.13542663X-RAY DIFFRACTION99
1.9615-2.15890.18091360.13012660X-RAY DIFFRACTION98
2.1589-2.47120.17291250.14332699X-RAY DIFFRACTION99
2.4712-3.11320.15951540.15792737X-RAY DIFFRACTION100
3.1132-37.17550.19231350.16082860X-RAY DIFFRACTION98

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