+Open data
-Basic information
Entry | Database: PDB / ID: 3w06 | ||||||
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Title | Crystal structure of Arabidopsis thaliana DWARF14 Like (AtD14L) | ||||||
Components | Hydrolase, alpha/beta fold family protein | ||||||
Keywords | HYDROLASE / KARRIKIN SIGNALING / ALPHA/BETA HYDROLASE / KARRIKIN BINDING | ||||||
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: 1.15 Å | ||||||
Authors | Kagiyama, M. / Hirano, Y. / Mori, T. / Kim, S.Y. / Kyozuka, J. / Seto, Y. / Yamaguchi, S. / Hakoshima, T. | ||||||
Citation | Journal: Genes Cells / Year: 2013 Title: Structures of D14 and D14L in the strigolactone and karrikin signaling pathways Authors: Kagiyama, M. / Hirano, Y. / Mori, T. / Kim, S.Y. / Kyozuka, J. / Seto, Y. / Yamaguchi, S. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w06.cif.gz | 139.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w06.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 3w06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/3w06 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/3w06 | HTTPS FTP |
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-Related structure data
Related structure data | 3w04SC 3w05C 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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Unit cell |
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-Components
#1: Protein | Mass: 29970.076 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: PET49B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q9SZU7 | ||
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#2: Chemical | ChemComp-EDO / #3: 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: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0M AMMONIUM SULFATE, 0.2M BICINE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: May 18, 2011 / Details: mirrors |
Radiation | Monochromator: Rotated-inclined double-crystal monochromator , Si (111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. all: 94807 / Num. obs: 90920 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.069 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8782 / Rsym value: 0.535 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W04 Resolution: 1.15→47.83 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.942 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.826 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→47.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 20
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