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

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Basic information

Entry
Database: PDB / ID: 3stv
TitleCrystal Structure of tomato Methylketone Synthase I complexed with 3-hydroxyoctanoate
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
(3S)-3-hydroxyoctanoic acid / BROMIDE ION / Methylketone synthase I
Similarity search - Component
Biological speciesLycopersicon hirsutum f. glabratum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / Item: _software.name
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)58,5024
Polymers58,2622
Non-polymers2402
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-18 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.038, 92.380, 60.596
Angle α, β, γ (deg.)90.000, 97.560, 90.000
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-3HO / (3S)-3-hydroxyoctanoic acid


Mass: 160.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O3
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
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, 4 hr soak in 1mM 3-hydroxyoctanoate, 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: 0.97944 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2006
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.2→19.6 Å / Num. all: 26450 / Num. obs: 26450 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 27.97 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.2-2.33.10.5172.4910184932329599.1
2.3-2.50.443.116082511799.8
2.5-2.80.3044.5116290519099.2
2.8-3.010.216.67899251199.4
3.01-3.370.1418.949359297299.5
3.37-3.50.10611.72235476797.6
3.5-3.880.08213.735457175999
3.88-4.250.06217.373553115398.7
4.25-4.750.04822.053295105699
4.75-5.50.04521.98291994498.8
5.5-6.680.05320.21239875499.6
6.68-19.70.02633.12292893294.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YAS

7yas


Resolution: 2.2→19.6 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 1319 4.9 %RANDOM
Rwork0.2022 ---
all0.22 26450 --
obs0.222 26450 99.1 %-
Solvent computationBsol: 44.4552 Å2
Displacement parametersBiso max: 93.88 Å2 / Biso mean: 25.5093 Å2 / Biso min: 3.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.795 Å20 Å2-0.505 Å2
2---1.548 Å20 Å2
3---0.753 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3975 0 12 218 4205
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.9842
X-RAY DIFFRACTIONc_scbond_it3.0532.5
X-RAY DIFFRACTIONc_mcangle_it2.9943
X-RAY DIFFRACTIONc_scangle_it4.2784
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION33ho.par
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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