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- PDB-3sty: Crystal Structure of tomato Methylketone Synthase I T18A mutant -

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Basic information

Entry
Database: PDB / ID: 3sty
TitleCrystal Structure of tomato Methylketone Synthase I T18A mutant
ComponentsMethylketone synthase 1
KeywordsHYDROLASE / methylketone / alpha/beta hydrolase / decarboxylase
Function / homology
Function and homology information


Methylesterase/Alpha-hydroxynitrile lyase / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DECANOIC ACID / Methylketone synthase I
Similarity search - Component
Biological speciesLycopersicon hirsutum f. glabratum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAuldridge, M.E. / Austin, M.B. / Noel, J.P.
CitationJournal: Plant Cell / Year: 2012
Title: Emergent Decarboxylase Activity and Attenuation of alpha/beta-Hydrolase Activity during the Evolution of Methylketone Biosynthesis in Tomato.
Authors: Auldridge, M.E. / Guo, Y. / Austin, M.B. / Ramsey, J. / Fridman, E. / Pichersky, E. / Noel, J.P.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methylketone synthase 1
B: Methylketone synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5464
Polymers58,2022
Non-polymers3452
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-15 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.292, 106.182, 59.847
Angle α, β, γ (deg.)90.00, 96.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methylketone synthase 1


Mass: 29100.914 Da / Num. of mol.: 2 / Mutation: T18A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lycopersicon hirsutum f. glabratum (plant)
Gene: MKS1 / Plasmid: pHis9GW / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E0YCS2
#2: Chemical ChemComp-DKA / DECANOIC ACID / Capric acid


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MOPSO-Na+, 17.0% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2007 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.4 % / Number: 220588 / Rmerge(I) obs: 0.059 / Χ2: 1.31 / D res high: 1.7 Å / D res low: 50 Å / Num. obs: 64513 / % possible obs: 98
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.665098.810.0312.0943.4
2.913.669910.0462.5923.4
2.542.919910.0621.9913.5
2.312.5498.810.0731.4563.5
2.142.3198.610.0861.2213.4
2.022.1498.410.1150.9713.5
1.912.0297.610.1610.83.4
1.831.9197.510.2350.6843.5
1.761.8396.610.3360.6233.4
1.71.769610.4990.593.3
ReflectionResolution: 1.7→37.1 Å / Num. all: 64513 / Num. obs: 64470 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.059 / Net I/σ(I): 23.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Num. unique all: 6306 / Rsym value: 0.499 / % possible all: 96

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YAS

7yas


Resolution: 1.7→37.1 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.2134 3246 RANDOM
Rwork0.1962 --
all0.2063 64513 -
obs0.2007 64470 -
Solvent computationBsol: 49.4721 Å2
Displacement parametersBiso max: 60.98 Å2 / Biso mean: 23.9974 Å2 / Biso min: 7.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.739 Å20 Å22.141 Å2
2---3.51 Å20 Å2
3----0.228 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3965 0 24 376 4365
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6752
X-RAY DIFFRACTIONc_mcangle_it2.4663
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3dC3.par

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