+Open data
-Basic information
Entry | Database: PDB / ID: 4hrx | ||||||
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Title | Crystal structure of KAI2 | ||||||
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: 2.11 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 | 4hrx.cif.gz | 69 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hrx.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hrx_validation.pdf.gz | 407.4 KB | Display | wwPDB validaton report |
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Full document | 4hrx_full_validation.pdf.gz | 407.3 KB | Display | |
Data in XML | 4hrx_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 4hrx_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/4hrx ftp://data.pdbj.org/pub/pdb/validation_reports/hr/4hrx | HTTPS FTP |
-Related structure data
Related structure data | 4hryC 4htaC 1womS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: AT4g37470, F6G17.120 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9SZU7 |
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#2: 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: 2.07 Å3/Da / Density % sol: 40.6 % |
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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: 2.11→56.04 Å / Num. all: 15121 / Num. obs: 14659 / % possible obs: 97.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.11→2.23 Å / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1WOM Resolution: 2.11→47.07 Å / Cor.coef. Fo:Fc: 0.9386 / Cor.coef. Fo:Fc free: 0.9182 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.218 / Cross valid method: THROUGHOUT / σ(F): 32 / SU R Blow DPI: 0.232 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.173 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 85.23 Å2 / Biso mean: 22.19 Å2 / Biso min: 7.64 Å2
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Refine analyze | Luzzati coordinate error obs: 0.205 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→47.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.28 Å / Total num. of bins used: 7
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