+Open data
-Basic information
Entry | Database: PDB / ID: 4ih9 | ||||||
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Title | Crystal structure of rice DWARF14 (D14) | ||||||
Components | Dwarf 88 esterase | ||||||
Keywords | HYDROLASE / strigolactone receptor / alpha/beta hydrolase | ||||||
Function / homology | Function and homology information strigolactone biosynthetic process / secondary shoot formation / Hydrolases; Acting on ester bonds / hydrolase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Cell Res. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ih9.cif.gz | 118.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ih9.ent.gz | 91.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ih9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/4ih9 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/4ih9 | HTTPS FTP |
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-Related structure data
Related structure data | 4ih1SC 4ih4C 4ihaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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.) Oryza sativa Japonica Group (Japanese rice) Gene: D14, D88, LOC_Os03g10620, Os03g0203200 / Plasmid: pETDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q10QA5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.12 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
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→40 Å / Num. all: 76211 / Num. obs: 76002 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IH1 Resolution: 1.55→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.338 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.083 / ESU R Free: 0.079 / 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: 53.15 Å2 / Biso mean: 15.7356 Å2 / Biso min: 5.79 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→40 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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