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- PDB-3stx: Crystal Structure of tomato Methylketone Synthase I H243A variant... -

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Basic information

Entry
Database: PDB / ID: 3stx
TitleCrystal Structure of tomato Methylketone Synthase I H243A variant complexed with beta-ketoheptanoate
ComponentsMethylketone synthase 1
KeywordsHYDROLASE / methylketone / alpha/beta hydrolase / decarboxylase
Function / homology
Function and homology information


jasmonic acid metabolic process / methyl salicylate esterase activity / methyl indole-3-acetate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process
Similarity search - Function
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
3-oxoheptanoic acid / Methylketone synthase I
Similarity search - Component
Biological speciesLycopersicon hirsutum f. glabratum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,4164
Polymers58,1282
Non-polymers2882
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-17 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.237, 94.387, 60.077
Angle α, β, γ (deg.)90.000, 97.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methylketone synthase 1


Mass: 29063.871 Da / Num. of mol.: 2 / Mutation: H243A
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-BKA / 3-oxoheptanoic acid


Mass: 144.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H12O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M MOPSO-Na+, 15% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, overnight soak in 1mM beta-ketoheptanoate, pH 7.0, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 25, 2007
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→19.6 Å / Num. all: 21097 / Num. obs: 21096 / % possible obs: 88.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 32.115 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.3-2.44.10.5312.75108542668266894.2
100332335
167894139
107492519
126182984
1256369
52261363
4057991
44171057
3972963
3093764
3954945

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
BOSdata collection
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YAS

7yas


Resolution: 2.3→19.37 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.862 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.738 / SU ML: 0.211 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 1083 5.1 %RANDOM
Rwork0.2052 ---
all0.235 21097 --
obs0.2086 21093 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.97 Å2 / Biso mean: 28.3783 Å2 / Biso min: 2.93 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 20 160 4124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224056
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9895510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20825.07142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44115701
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.444158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212962
X-RAY DIFFRACTIONr_mcbond_it0.4761.52580
X-RAY DIFFRACTIONr_mcangle_it0.86524183
X-RAY DIFFRACTIONr_scbond_it0.88531476
X-RAY DIFFRACTIONr_scangle_it1.4454.51326
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 88 -
Rwork0.292 1483 -
all-1571 -
obs--100 %

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