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- PDB-4iha: Crystal structure of rice DWARF14 (D14) in complex with a GR24 hy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iha | ||||||
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Title | Crystal structure of rice DWARF14 (D14) in complex with a GR24 hydrolysis intermediate | ||||||
![]() | Dwarf 88 esterase | ||||||
![]() | HYDROLASE / strigolactone / GR24 hydrolysis / alpha/beta hydrolase | ||||||
Function / homology | ![]() strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm 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 | ![]() | 123.4 KB | Display | ![]() |
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PDB format | ![]() | 95.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 460.8 KB | Display | |
Data in XML | ![]() | 26.4 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ih1C ![]() 4ih4C ![]() 4ih9C ![]() 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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2 | ![]()
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Unit cell |
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Details | There are two molecules in an a.u. But no significant interaction interface between the two molecules. |
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Components
#1: Protein | Mass: 29349.707 Da / Num. of mol.: 2 / Fragment: UNP residues 51-318 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: D14, D88, LOC_Os03g10620, Os03g0203200 / Plasmid: pETDuet1 / 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: 2.15 Å3/Da / Density % sol: 42.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG6000, MPD, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 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. obs: 110233 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.107 / Χ2: 1.05 / Net I/σ(I): 5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1WOM Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.462 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.082 / 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: 58.05 Å2 / Biso mean: 20.4594 Å2 / Biso min: 6.98 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: 1.55→1.59 Å / Total num. of bins used: 20
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