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Open data
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Basic information
Entry | Database: PDB / ID: 8vd1 | ||||||
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Title | Crystal Structure of KAI2 from Oryza sativa with MPD | ||||||
![]() | Probable esterase D14L | ||||||
![]() | HYDROLASE / Karrikin / signalling / alpha/beta-hydrolase / rice | ||||||
Function / homology | arbuscular mycorrhizal association / response to karrikin / Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / nucleus / cytoplasm / Probable esterase D14L![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gilio, A.K. / Shabek, N. / Guercio, A.M. / Pawlak, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into rice KAI2 receptor provide functional implications for perception and signal transduction. Authors: Guercio, A.M. / Gilio, A.K. / Pawlak, J. / Shabek, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.1 KB | Display | ![]() |
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PDB format | ![]() | 50.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8vczC ![]() 8vd3C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 29746.975 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MPD / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Sodium HEPES, 0.1M MOPS (acid) pH 7.5, 0.018M Magnesium chloride hexahydrate, 0.018M Calcium chloride dihydrate, 9.4% v/v MPD, 9.4% v/v PEG 1000, 9.4% v/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 24, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999992 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→40.49 Å / Num. obs: 64764 / % possible obs: 99.3 % / Redundancy: 4.3 % / Rsym value: 0.051 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.29→1.31 Å / Num. unique obs: 2848 / Rsym value: 0.32 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.478 Å2
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Refinement step | Cycle: 1 / Resolution: 1.29→40.49 Å
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Refine LS restraints |
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