+Open data
-Basic information
Entry | Database: PDB / ID: 5zcu | ||||||
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Title | Crystal structure of RCAR3:PP2C wild-type with pyrabactin | ||||||
Components |
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Keywords | PLANT PROTEIN / Complex / PP2C / ABA receptor / pyrabactin / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information negative regulation of protein serine/threonine phosphatase activity / 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 ...negative regulation of protein serine/threonine phosphatase activity / 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 / metal ion binding / nucleus / 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: 2.413 Å | ||||||
Authors | Han, S. / Lee, Y. / Lee, S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Plant Mol.Biol. / Year: 2019 Title: Structural determinants for pyrabactin recognition in ABA receptors in Oryza sativa. Authors: Han, S. / Lee, Y. / Park, E.J. / Min, M.K. / Lee, Y. / Kim, T.H. / Kim, B.G. / Lee, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zcu.cif.gz | 372 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zcu.ent.gz | 301.2 KB | Display | PDB format |
PDBx/mmJSON format | 5zcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/5zcu ftp://data.pdbj.org/pub/pdb/validation_reports/zc/5zcu | HTTPS FTP |
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-Related structure data
Related structure data | 5gwpS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 35578.594 Da / Num. of mol.: 2 / Mutation: E139A/E140A/K142A 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 |
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-Non-polymers , 4 types, 133 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: 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: 2.32 Å3/Da / Density % sol: 46.97 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, ammonium sulfate, sucrose / PH range: 4-6 |
-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: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2017 |
Radiation | Monochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→38.496 Å / Num. obs: 36217 / % possible obs: 93.42 % / Redundancy: 4.6 % / Biso Wilson estimate: 24.89 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.09655 / Rpim(I) all: 0.04937 / Net I/σ(I): 18.72 |
Reflection shell | Resolution: 2.45→2.538 Å / Rmerge(I) obs: 0.5903 / Num. unique obs: 3212 / CC1/2: 0.675 / Rpim(I) all: 0.2984 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GWP Resolution: 2.413→38.496 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.413→38.496 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: -22.7217 Å / Origin y: 13.6326 Å / Origin z: 58.3623 Å
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Refinement TLS group | Selection details: all |