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- PDB-4ih1: Crystal structure of Karrikin Insensitive 2 (KAI2) from Arabidops... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ih1 | ||||||
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Title | Crystal structure of Karrikin Insensitive 2 (KAI2) from Arabidopsis thaliana | ||||||
![]() | Hydrolase, alpha/beta fold family protein | ||||||
![]() | HYDROLASE / Karrikin receptor / alpha/beta hydrolase | ||||||
Function / homology | ![]() de-etiolation / response to karrikin / photomorphogenesis / hydrolase activity / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, X.E. / Zhao, L.-H. / Wu, Z.-S. / Yi, W. / Li, S. / Li, Y. / Xu, Y. / Xu, T.-H. / Liu, Y. / Chen, R.-Z. ...Zhou, X.E. / Zhao, L.-H. / Wu, Z.-S. / Yi, W. / Li, S. / Li, Y. / Xu, Y. / Xu, T.-H. / Liu, Y. / Chen, R.-Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Zhang, C. / Melcher, K. / Xu, H.E. | ||||||
![]() | ![]() Title: Crystal structures of two phytohormone signal-transducing alpha / beta hydrolases: karrikin-signaling KAI2 and strigolactone-signaling DWARF14. Authors: Zhao, L.H. / Zhou, X.E. / Wu, Z.S. / Yi, W. / Xu, Y. / Li, S. / Xu, T.H. / Liu, Y. / Chen, R.Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Xie, C. / Song, W. / Zhong, D. / Xu, Y. / Wang, Y. ...Authors: Zhao, L.H. / Zhou, X.E. / Wu, Z.S. / Yi, W. / Xu, Y. / Li, S. / Xu, T.H. / Liu, Y. / Chen, R.Z. / Kovach, A. / Kang, Y. / Hou, L. / He, Y. / Xie, C. / Song, W. / Zhong, D. / Xu, Y. / Wang, Y. / Li, J. / Zhang, C. / Melcher, K. / Xu, H.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.1 KB | Display | ![]() |
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PDB format | ![]() | 47.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.8 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ih4C ![]() 4ih9C ![]() 4ihaC ![]() 1womS 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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1 |
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Unit cell |
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Details | biological unit is the same as asym. |
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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: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG400, ammonium sulfate, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→30 Å / Num. all: 39492 / Num. obs: 39492 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.099 / Χ2: 1.093 / Net I/σ(I): 8.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WOM Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.385 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.08 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66 Å2 / Biso mean: 24.3917 Å2 / Biso min: 11.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.551→1.591 Å / Total num. of bins used: 20
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