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Yorodumi- PDB-4la7: X-ray crystal structure of the PYL2-quinabactin-Hab1 ternary complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4la7 | ||||||
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Title | X-ray crystal structure of the PYL2-quinabactin-Hab1 ternary complex | ||||||
Components |
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Keywords | Hydrolase/receptor/inhibitor / PYL2 / HAB1 / PP2C inhibition / Hydrolase-receptor-inhibitor complex | ||||||
Function / homology | Function and homology information 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 / signaling receptor activity / protein homodimerization activity / identical protein binding ...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 / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å | ||||||
Authors | Peterson, F.C. / Volkman, B.F. / Cutler, S.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Activation of dimeric ABA receptors elicits guard cell closure, ABA-regulated gene expression, and drought tolerance. Authors: Okamoto, M. / Peterson, F.C. / Defries, A. / Park, S.Y. / Endo, A. / Nambara, E. / 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 | 4la7.cif.gz | 215.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4la7.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 4la7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4la7 ftp://data.pdbj.org/pub/pdb/validation_reports/la/4la7 | HTTPS FTP |
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-Related structure data
Related structure data | 3kb3S 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 21592.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g26040, PYL2, RCAR14, T19L18.15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O80992 |
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#2: Protein | Mass: 36582.891 Da / Num. of mol.: 1 / Fragment: unp residues 178-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) Gene: At1g72770, F28P22.4, HAB1, HAB1 (Residues 179-511), P2C-HA Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase |
-Non-polymers , 5 types, 331 molecules
#3: Chemical | ChemComp-A1O / | ||||
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#4: Chemical | ChemComp-ACT / | ||||
#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-GOL / | #7: 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: 2.54 Å3/Da / Density % sol: 51.57 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris, 160 mM Magnesium chloride, 20% (v/v) PEG-8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 77 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2011 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.98→50 Å / Num. obs: 41105 / % possible obs: 97.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 23.76 Å2 / Rmerge(I) obs: 0.088 / Χ2: 0.883 / Net I/σ(I): 6.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KB3 Resolution: 1.98→49.266 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8322 / SU ML: 0.51 / σ(F): 0 / Phase error: 23.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.274 Å2 / ksol: 0.338 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.09 Å2 / Biso mean: 34.4425 Å2 / Biso min: 10.59 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→49.266 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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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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