+Open data
-Basic information
Entry | Database: PDB / ID: 5zcl | ||||||||||||
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Title | Crystal structure of OsPP2C50 I267L: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 / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) Oryza sativa (Asian cultivated rice) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.661 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 | 5zcl.cif.gz | 202.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zcl.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 5zcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/5zcl ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zcl | HTTPS FTP |
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-Related structure data
Related structure data | 5zcgC 5zchC 5gwpS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35578.594 Da / Num. of mol.: 2 / Mutation: E139A/E140A/K142A/I267L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: 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 (Asian cultivated rice) / Production host: Escherichia coli (E. coli) / References: UniProt: K4N2F7, UniProt: Q6EN42*PLUS #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: 3.17 Å3/Da / Density % sol: 61.21 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 12% (w/v) PEG 8000, 0.3M Mg(OAc)2, 0.1M MES pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 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: 2.661→38.149 Å / Num. obs: 39539 / % possible obs: 99.27 % / Redundancy: 4.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.1204 / Rpim(I) all: 0.0662 / Net I/σ(I): 9.22 |
Reflection shell | Resolution: 2.661→2.757 Å / Rmerge(I) obs: 0.708 / Num. unique obs: 3799 / CC1/2: 0.648 / Rpim(I) all: 0.4107 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GWP Resolution: 2.661→38.149 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.661→38.149 Å
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Refine LS restraints |
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LS refinement shell |
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