+Open data
-Basic information
Entry | Database: PDB / ID: 5gwp | ||||||
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Title | Crystal structure of RCAR3:PP2C wild-type with (+)-ABA | ||||||
Components |
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Keywords | HYDROLASE/RECEPTOR / abscisic acid / ABA receptor / PP2C / HYDROLASE-RECEPTOR complex | ||||||
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: 2.577 Å | ||||||
Authors | Han, S. / Lee, S. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Mol Plant / Year: 2017 Title: Modulation of ABA Signaling by Altering VxG Phi L Motif of PP2Cs in Oryza sativa. Authors: Han, S. / Min, M.K. / Lee, S.Y. / Lim, C.W. / Bhatnagar, N. / Lee, Y. / Shin, D. / Chung, K.Y. / Lee, S.C. / 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 | 5gwp.cif.gz | 369.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gwp.ent.gz | 302.2 KB | Display | PDB format |
PDBx/mmJSON format | 5gwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gwp ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gwp | HTTPS FTP |
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-Related structure data
Related structure data | 5gwoC 3rt0S C: citing same article (ref.) 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
#1: Protein | Mass: 35507.512 Da / Num. of mol.: 2 / Fragment: UNP residues 59-385 / 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 / Fragment: UNP residues 30-204 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: 2.16 Å3/Da / Density % sol: 42.96 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 8000, MES pH 6.0, calcium acetate |
-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: Oct 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.577→46.1435 Å / Num. obs: 30728 / % possible obs: 96 % / Redundancy: 11 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1142 / Rsym value: 0.12 / Net I/σ(I): 22.02 |
Reflection shell | Resolution: 2.577→2.67 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RT0 Resolution: 2.577→46.136 Å / SU ML: 0.34 / Cross valid method: NONE / σ(F): 0 / Phase error: 27.25 / 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: 2.577→46.136 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: -38.7842 Å / Origin y: -13.2151 Å / Origin z: -23.3851 Å
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Refinement TLS group | Selection details: all |