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- PDB-3stt: Crystal Structure of tomato Methylketone Synthase I Apo form -

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Basic information

Entry
Database: PDB / ID: 3stt
TitleCrystal Structure of tomato Methylketone Synthase I Apo form
ComponentsMethylketone synthase I
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
DECANOIC ACID / Methylketone synthase I
Similarity search - Component
Biological speciesLycopersicon hirsutum f. glabratum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 I
B: Methylketone synthase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6064
Polymers58,2622
Non-polymers3452
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-16 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.179, 105.454, 59.836
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methylketone synthase I


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.: 2 / Source method: obtained synthetically / Formula: C10H20O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
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, 3% sucrose, 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: BL1-5 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2005
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: 2.24→47.9 Å / Num. all: 27180 / Num. obs: 27180 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 35.7 Å2 / Rsym value: 0.041 / Χ2: 1.262 / Net I/σ(I): 33.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allRsym valueΧ2% possible all
2.24-2.283.50.16212430.1621.42387.4
2.28-2.323.60.14713091.36892
2.32-2.363.60.13513131.32693.3
2.36-2.413.60.13213351.32192.3
2.41-2.473.60.11612891.3692.9
2.47-2.523.60.09813641.35294.1
2.52-2.593.60.09313351.38594.2
2.59-2.663.70.07913291.28594.7
2.66-2.733.60.07413671.30296.3
2.73-2.823.70.06513931.28496.7
2.82-2.923.70.05613711.29597.7
2.92-3.043.70.05214161.31698.1
3.04-3.183.80.04314151.28898.6
3.18-3.353.80.03913941.25298.8
3.35-3.563.80.03314151.18998.9
3.56-3.833.90.02914131.19498.7
3.83-4.223.80.02514181.06799.4
4.22-4.823.80.02414501.08299.2
4.82-6.083.80.02614321.00199.5
6.08-47.93.70.02714341.28997.9

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Processing

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

7yas


Resolution: 2.24→47.9 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.221 1364 RANDOM
Rwork0.1812 --
all0.199 27180 -
obs0.189 27180 -
Displacement parametersBiso max: 63.05 Å2 / Biso mean: 25.9422 Å2 / Biso min: 3.95 Å2
Refinement stepCycle: LAST / Resolution: 2.24→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 24 260 4253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.39693

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