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Yorodumi- PDB-4wvo: An engineered PYR1 mandipropamid receptor in complex with mandipr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wvo | ||||||
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Title | An engineered PYR1 mandipropamid receptor in complex with mandipropamid and HAB1 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INTHIBITOR / PYR/PYL/RCAR / PYR1 / Hab1 / mandipropamid / PP2C inhibitor / HYDROLASE-HYDROLASE INTHIBITOR complex | ||||||
Function / homology | Function and homology information positive regulation of response to water deprivation / plant-type vacuole membrane / regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase ...positive regulation of response to water deprivation / plant-type vacuole membrane / regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / ubiquitin-like protein ligase binding / signaling receptor activity / protein homodimerization activity / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.251 Å | ||||||
Authors | Peterson, F.C. / Volkman, B.F. / Cutler, S.R. | ||||||
Citation | Journal: Nature / Year: 2015 Title: Agrochemical control of plant water use using engineered abscisic acid receptors. Authors: Park, S.Y. / Peterson, F.C. / Mosquna, A. / Yao, J. / Volkman, B.F. / Cutler, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wvo.cif.gz | 208.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wvo.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/4wvo ftp://data.pdbj.org/pub/pdb/validation_reports/wv/4wvo | HTTPS FTP |
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-Related structure data
Related structure data | 3qn1S 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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Unit cell |
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-Components
#1: Protein | Mass: 20659.332 Da / Num. of mol.: 1 / Mutation: K59R V81I F108A F159L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYR1, ABIP6, RCAR11, At4g17870, T6K21.50 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O49686 | ||
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#2: Protein | Mass: 36582.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HAB1, P2C-HA, At1g72770, F28P22.4 / Plasmid: pET11M / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase | ||
#3: Chemical | ChemComp-3UZ / ( | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22.5% PEG 2000 mono methyl ether 150 mM Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 25330 / % possible obs: 98.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 2.25→2.31 Å / Redundancy: 6 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.1 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3QN1 Resolution: 2.251→36.191 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.34 / 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: 2.251→36.191 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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