+Open data
-Basic information
Entry | Database: PDB / ID: 3stt | ||||||
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Title | Crystal Structure of tomato Methylketone Synthase I Apo form | ||||||
Components | Methylketone synthase I | ||||||
Keywords | HYDROLASE / 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 | ||||||
Biological species | Lycopersicon hirsutum f. glabratum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | ||||||
Authors | Auldridge, M.E. / Austin, M.B. / Noel, J.P. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3stt.cif.gz | 115.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3stt.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 3stt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/3stt ftp://data.pdbj.org/pub/pdb/validation_reports/st/3stt | HTTPS FTP |
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-Related structure data
Related structure data | 3stuC 3stvC 3stwC 3stxC 3styC 7yasS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.55 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 30, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YAS Resolution: 2.24→47.9 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Displacement parameters | Biso max: 63.05 Å2 / Biso mean: 25.9422 Å2 / Biso min: 3.95 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→47.9 Å
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Refine LS restraints |
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