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- PDB-3stw: Crystal Structure of tomato Methylketone Synthase I complexed wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3stw | ||||||
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Title | Crystal Structure of tomato Methylketone Synthase I complexed with 2-tridecanone | ||||||
![]() | Methylketone synthase 1 | ||||||
![]() | HYDROLASE / methylketone / alpha/beta hydrolase / decarboxylase | ||||||
Function / homology | ![]() jasmonic acid metabolic process / methyl salicylate esterase activity / methyl jasmonate esterase activity / salicylic acid metabolic process / methyl indole-3-acetate esterase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Auldridge, M.E. / Austin, M.B. / Noel, J.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115 KB | Display | ![]() |
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PDB format | ![]() | 88 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.1 KB | Display | ![]() |
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Full document | ![]() | 458.7 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sttC ![]() 3stuC ![]() 3stvC ![]() 3stxC ![]() 3styC ![]() 7yasS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: MKS1 / Plasmid: pHis9GW / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M PIPES-Na+, 17% (w/v) PEG 8000, 0.3M NaBr, 2mM dithiothreitol, overnight soak in 1mM 2-tridecanone, pH 6.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.31→20 Å / Num. all: 30189 / Num. obs: 26600 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 27.452 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.52 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7YAS Resolution: 2.31→20 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 28.0365 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.02 Å2 / Biso mean: 24.82 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→20 Å
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Refine LS restraints |
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Xplor file |
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