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- PDB-3nmv: Crystal structure of pyrabactin-bound abscisic acid receptor PYL2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nmv | ||||||
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Title | Crystal structure of pyrabactin-bound abscisic acid receptor PYL2 mutant A93F in complex with type 2C protein phosphatase ABI2 | ||||||
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![]() | PROTEIN BINDING / PYL2 / Pyrabactin / Abscisic acid receptor / helix-grip fold / type 2C protein phosphatase | ||||||
Function / homology | ![]() photoinhibition / negative regulation of abscisic acid-activated signaling pathway / regulation of stomatal opening / protein phosphatase inhibitor complex / response to water deprivation / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity ...photoinhibition / negative regulation of abscisic acid-activated signaling pathway / regulation of stomatal opening / protein phosphatase inhibitor complex / response to water deprivation / response to abscisic acid / abscisic acid binding / abscisic acid-activated signaling pathway / response to osmotic stress / protein phosphatase inhibitor activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / negative regulation of protein kinase activity / signaling receptor activity / response to heat / protein homodimerization activity / identical protein binding / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, X.E. / Melcher, K. / Ng, L.-M. / Soon, F.-F. / Xu, Y. / Suino-Powell, K.M. / Kovach, A. / Li, J. / Yong, E.-L. / Xu, H.E. | ||||||
![]() | ![]() Title: Identification and mechanism of ABA receptor antagonism. Authors: Melcher, K. / Xu, Y. / Ng, L.M. / Zhou, X.E. / Soon, F.F. / Chinnusamy, V. / Suino-Powell, K.M. / Kovach, A. / Tham, F.S. / Cutler, S.R. / Li, J. / Yong, E.L. / Zhu, J.K. / Xu, H.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.3 KB | Display | ![]() |
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PDB format | ![]() | 159.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 995.6 KB | Display | ![]() |
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Full document | ![]() | 1011.8 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nmhC ![]() 3nmnC ![]() 3nmpC ![]() 3nmtSC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20096.600 Da / Num. of mol.: 1 / Mutation: A93F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 35783.980 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O04719, protein-serine/threonine phosphatase | ||
#3: Chemical | ChemComp-PYV / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 66.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, 10% PEG 8000, 10% sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 44745 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 32.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3NMT Resolution: 2.1→29.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.592 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.284 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.158 Å / Total num. of bins used: 20
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