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Open data
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Basic information
Entry | Database: PDB / ID: 5z9g | ||||||
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Title | Crystal structure of KAI2 | ||||||
![]() | Probable esterase KAI2 | ||||||
![]() | HYDROLASE / alpha/beta hydrolase | ||||||
Function / homology | ![]() de-etiolation / response to karrikin / photomorphogenesis / hydrolase activity / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, K.L. / Cha, J.S. / Soh, M.S. / Cho, H.S. | ||||||
![]() | ![]() Title: A missense allele of KARRIKIN-INSENSITIVE2 impairs ligand-binding and downstream signaling in Arabidopsis thaliana. Authors: Lee, I. / Kim, K. / Lee, S. / Lee, S. / Hwang, E. / Shin, K. / Kim, D. / Choi, J. / Choi, H. / Cha, J.S. / Kim, H. / Lee, R.A. / Jeong, S. / Kim, J. / Kim, Y. / Nam, H.G. / Park, S.K. / Cho, H.S. / Soh, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.1 KB | Display | ![]() |
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PDB format | ![]() | 94.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429 KB | Display | ![]() |
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Full document | ![]() | 432.6 KB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5z9hC ![]() 1womS S: Starting model for refinement C: citing same article ( |
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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: 29815.916 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion / pH: 7.5 / Details: 1M Na-citrate, 100 mM HEPES (pH 7.5), 5% glycerol |
-Data collection
Diffraction | Mean temperature: 93.1 K / Ambient temp details: liquid nitrogen stream |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. obs: 43387 / % possible obs: 99.7 % / Redundancy: 6.1 % / Net I/σ(I): 54.1 |
Reflection shell | Resolution: 1.49→1.52 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WOM Resolution: 1.49→47.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.801 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.743 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→47.64 Å
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Refine LS restraints |
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