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

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Basic information

Entry
Database: PDB / ID: 5gtg
TitleCrystal structure of onion lachrymatory factor synthase (LFS) containing 1,2-propanediol
ComponentsLachrymatory-factor synthase
KeywordsISOMERASE / SRPBCC / helix-grip fold / cytosolic
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
trehalose / S-1,2-PROPANEDIOL / Lachrymatory-factor synthase
Similarity search - Component
Biological speciesAllium cepa (onion)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsArakawa, T. / Sato, Y. / 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. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lachrymatory-factor synthase
B: Lachrymatory-factor synthase
C: Lachrymatory-factor synthase
D: Lachrymatory-factor synthase
E: Lachrymatory-factor synthase
F: Lachrymatory-factor synthase
G: Lachrymatory-factor synthase
H: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,27916
Polymers159,2458
Non-polymers1,0348
Water10,521584
1
A: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3243
Polymers19,9061
Non-polymers4182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7380 Å2
MethodPISA
2
B: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3695
Polymers19,9061
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area7440 Å2
MethodPISA
3
C: Lachrymatory-factor synthase


Theoretical massNumber of molelcules
Total (without water)19,9061
Polymers19,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7550 Å2
MethodPISA
4
D: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9822
Polymers19,9061
Non-polymers761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7450 Å2
MethodPISA
5
E: Lachrymatory-factor synthase


Theoretical massNumber of molelcules
Total (without water)19,9061
Polymers19,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7400 Å2
MethodPISA
6
F: Lachrymatory-factor synthase


Theoretical massNumber of molelcules
Total (without water)19,9061
Polymers19,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7360 Å2
MethodPISA
7
G: Lachrymatory-factor synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9822
Polymers19,9061
Non-polymers761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7410 Å2
MethodPISA
8
H: Lachrymatory-factor synthase


Theoretical massNumber of molelcules
Total (without water)19,9061
Polymers19,9061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.858, 172.858, 64.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein / Sugars , 2 types, 9 molecules ABCDEFGH

#1: Protein
Lachrymatory-factor synthase


Mass: 19905.580 Da / Num. of mol.: 8
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: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 591 molecules

#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 584 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2016
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.501
11-H, K, -L20.499
ReflectionResolution: 1.7→50 Å / Num. obs: 204662 / % possible obs: 97.3 % / Redundancy: 6.1 % / Net I/σ(I): 19.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.2 / CC1/2: 0.86 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5GTF

5gtf


Resolution: 1.7→47.94 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.887 / SU B: 1.58 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TWIN REFINEMENT HAS BEEN APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.25979 10237 5 %RANDOM
Rwork0.22977 ---
obs0.23128 194424 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.053 Å2
Baniso -1Baniso -2Baniso -3
1-5.77 Å20 Å20 Å2
2--5.77 Å20 Å2
3----11.55 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9640 0 65 584 10289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0199956
X-RAY DIFFRACTIONr_bond_other_d0.0030.029207
X-RAY DIFFRACTIONr_angle_refined_deg2.8211.93713463
X-RAY DIFFRACTIONr_angle_other_deg1.416321349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.38851184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.84125.263456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.479151752
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5041516
X-RAY DIFFRACTIONr_chiral_restr0.1870.21450
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0210976
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022240
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_it2.5341.9114760
X-RAY DIFFRACTIONr_mcbond_other2.5321.9114759
X-RAY DIFFRACTIONr_mcangle_it3.2832.8595936
X-RAY DIFFRACTIONr_mcangle_other3.2832.8595937
X-RAY DIFFRACTIONr_scbond_it2.7532.0645196
X-RAY DIFFRACTIONr_scbond_other2.7532.0645196
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5943.0337528
X-RAY DIFFRACTIONr_long_range_B_refined5.03122.99111736
X-RAY DIFFRACTIONr_long_range_B_other5.02422.8711636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 582 -
Rwork0.325 11307 -
obs--76.72 %

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