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- PDB-3stu: Crystal Structure of tomato Methylketone Synthase I complexed wit... -

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Basic information

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


methyl indole-3-acetate esterase activity / methyl jasmonate esterase activity / jasmonic acid metabolic process / methyl salicylate 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
methyl (3S)-3-hydroxydodecanoate / DECANOIC ACID / Methylketone synthase I
Similarity search - Component
Biological speciesLycopersicon hirsutum f. glabratum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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)58,6644
Polymers58,2622
Non-polymers4032
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.197, 105.716, 59.888
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methylketone synthase 1


Mass: 29130.938 Da / Num. of mol.: 2
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


Mass: 172.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O2
#3: Chemical ChemComp-DK3 / methyl (3S)-3-hydroxydodecanoate


Mass: 230.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M PIPES-Na+, 22% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, 2 hr soak in 1mM methyl-3-hydroxydodecanoate, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 31, 2005
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.93→39.5 Å / Num. all: 44670 / Num. obs: 43407 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 36.59 Å2 / Rmerge(I) obs: 0.063 / Χ2: 2.151 / Net I/σ(I): 24.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRsym valueΧ2% possible all
1.93-1.973.50.49928750.4993.38598.7
1.97-2.023.80.30329961.944100
2.02-2.083.70.27429652.47299.5
2.08-2.143.80.229682.08199.9
2.14-2.213.80.15529781.92299.9
2.21-2.292.70.15121943.19573.7
2.29-2.383.80.11429611.747100
2.38-2.493.80.09729512.09399.8
2.49-2.623.80.0829832.11899.9
2.62-2.783.80.07129752.24799.5
2.78-33.80.06129772.03499.5
3-3.33.80.05529492.1399.6
3.3-3.783.60.05529452.12498.2
3.78-4.763.70.04129951.73199.7
4.76-503.70.04830401.77199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YAS

7yas


Resolution: 1.93→39.5 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.149 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2423 2186 5 %RANDOM
Rwork0.2149 ---
all0.238 44670 --
obs0.2163 43407 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.72 Å2 / Biso mean: 29.1645 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.93→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 28 246 4243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224099
X-RAY DIFFRACTIONr_angle_refined_deg1.0421.9875567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1795519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86425.068146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94315707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.222158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2654
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212986
X-RAY DIFFRACTIONr_mcbond_it0.4951.52594
X-RAY DIFFRACTIONr_mcangle_it0.93924208
X-RAY DIFFRACTIONr_scbond_it1.16531505
X-RAY DIFFRACTIONr_scangle_it1.9594.51357
LS refinement shellResolution: 1.931→1.981 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 144 -
Rwork0.353 --
obs--93.9 %

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