+Open data
-Basic information
Entry | Database: PDB / ID: 5zch | ||||||||||||
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Title | Crystal structure of OsPP2C50 I267W:OsPYL/RCAR3 with (+)-ABA | ||||||||||||
Components |
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Keywords | PLANT PROTEIN / abscisic acid / ABA / receptor / phosphatase / stress / complex | ||||||||||||
Function / homology | Function and homology information : / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / response to cold ...: / seed germination / response to water deprivation / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / response to cold / signaling receptor activity / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.474 Å | ||||||||||||
Authors | Lee, S. / Han, S. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Plant Mol.Biol. / Year: 2019 Title: Comprehensive survey of the VxG Phi L motif of PP2Cs from Oryza sativa reveals the critical role of the fourth position in regulation of ABA responsiveness. Authors: Han, S. / Lee, J.Y. / Lee, Y. / Kim, T.H. / Lee, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zch.cif.gz | 373.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zch.ent.gz | 302.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zch_validation.pdf.gz | 1019.6 KB | Display | wwPDB validaton report |
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Full document | 5zch_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5zch_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 5zch_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/5zch ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zch | HTTPS FTP |
-Related 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: 35651.645 Da / Num. of mol.: 2 / Mutation: E139A/E140A/K142A/I267W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: PP2C50, ABIL3, Os05g0537400, LOC_Os05g46040, OJ1741_B01.18, OSJNBa0052K01.2 Production host: Escherichia coli (E. coli) References: UniProt: Q6L5H6, protein-serine/threonine phosphatase #2: Protein | Mass: 20060.865 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: PYL3, PYL10, RCAR3, Os02g0255500, LOC_Os02g15640, OSJNBa0052K15.19, P0613F08.1 Production host: Escherichia coli (E. coli) / References: UniProt: Q6EN42 #3: Chemical | ChemComp-MG / #4: Chemical | #5: 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: 3.14 Å3/Da / Density % sol: 60.86 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 20% v/v PEG 400, 5% w/v PEG 3000, 10% v/v glycerol, 0.1M HEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.474→24.788 Å / Num. obs: 45783 / % possible obs: 96.87 % / Redundancy: 3.2 % / Net I/σ(I): 15.16 |
Reflection shell | Resolution: 2.474→2.563 Å |
-Processing
Software |
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Refinement | Resolution: 2.474→24.788 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.474→24.788 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.3507 Å / Origin y: -28.9149 Å / Origin z: -15.0559 Å
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Refinement TLS group | Selection details: all |