+Open data
-Basic information
Entry | Database: PDB / ID: 3kay | ||||||
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Title | Crystal structure of abscisic acid receptor PYL1 | ||||||
Components | Putative uncharacterized protein At5g46790 | ||||||
Keywords | SIGNALING PROTEIN / phytohormone receptor / PYR/PYL/RCAR / abscisic acid signaling | ||||||
Function / homology | Function and homology information regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / signaling receptor activity / protein homodimerization activity / identical protein binding ...regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / plastid / protein phosphatase inhibitor activity / defense response / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å | ||||||
Authors | Zhou, X.E. / Melcher, K. / Ng, L.-M. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.M. / Kovach, A. / Li, J. / Xu, H.E. | ||||||
Citation | Journal: Nature / Year: 2009 Title: Agate-latch-lock mechanism for hormone signalling by abscisic acid receptors Authors: Melcher, K. / Ng, L.-M. / Zhou, X.E. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.-M. / Park, S.-Y. / Weiner, J.J. / Fujii, H. / Chinnusamy, V. / Kovach, A. / Li, J. / Wang, Y. / Li, J.Y. / ...Authors: Melcher, K. / Ng, L.-M. / Zhou, X.E. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.-M. / Park, S.-Y. / Weiner, J.J. / Fujii, H. / Chinnusamy, V. / Kovach, A. / Li, J. / Wang, Y. / Li, J.Y. / Peterson, F.C. / Jensen, D.R. / Yong, E.-L. / Volkman, B.F. / Cutler, S.R. / Zhu, J.-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 | 3kay.cif.gz | 153.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kay.ent.gz | 123 KB | Display | PDB format |
PDBx/mmJSON format | 3kay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/3kay ftp://data.pdbj.org/pub/pdb/validation_reports/ka/3kay | 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: 20534.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g46790 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8VZS8 #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: 3.47 Å3/Da / Density % sol: 64.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG 4000, pH 7.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 16, 2009 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 28736 / Num. obs: 22196 / % possible obs: 72 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 22.5 % / Rsym value: 0.079 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 19.089 / SU ML: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å
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