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Yorodumi- PDB-4hta: The structure of the karrikin insensitive (KAI2) protein in Arabi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hta | ||||||
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Title | The structure of the karrikin insensitive (KAI2) protein in Arabidopsis thaliana | ||||||
Components | Hydrolase, alpha/beta fold family protein | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information de-etiolation / response to karrikin / photomorphogenesis / hydrolase activity / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å | ||||||
Authors | Bythell-Douglas, R. / Waters, M.T. / Scaffidi, A. / Flematti, G.R. / Smith, S.M. / Bond, C.S. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: The Structure of the Karrikin-Insensitive Protein (KAI2) in Arabidopsis thaliana Authors: Bythell-Douglas, R. / Waters, M.T. / Scaffidi, A. / Flematti, G.R. / Smith, S.M. / Bond, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hta.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hta.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 4hta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ht/4hta ftp://data.pdbj.org/pub/pdb/validation_reports/ht/4hta | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31972.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F6G17.120, AT4G37470 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SZU7 | ||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 1.5M sodium potassium phosphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9539 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9539 Å / Relative weight: 1 |
Reflection | Resolution: 1.901→77.62 Å / Num. all: 26147 / Num. obs: 26147 / % possible obs: 100 % / Biso Wilson estimate: 20.58 Å2 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→50.31 Å / Cor.coef. Fo:Fc: 0.9531 / Cor.coef. Fo:Fc free: 0.9479 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.101 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 92.78 Å2 / Biso mean: 22.48 Å2 / Biso min: 3.15 Å2
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Refine analyze | Luzzati coordinate error obs: 0.159 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.901→50.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.98 Å / Total num. of bins used: 13
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