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Yorodumi- PDB-3nmt: Crystal structure of pyrabactin bound abscisic acid receptor PYL2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nmt | ||||||
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Title | Crystal structure of pyrabactin bound abscisic acid receptor PYL2 mutant A93F in complex with type 2C protein phosphatase HAB1 | ||||||
Components |
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Keywords | PROTEIN BINDING / PYL2 / Pyrabactin / abscisic acid receptor / helix-grip fold | ||||||
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 / metal ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nmt.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nmt.ent.gz | 162.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/3nmt ftp://data.pdbj.org/pub/pdb/validation_reports/nm/3nmt | HTTPS FTP |
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-Related structure data
Related structure data | 3nmhC 3nmnC 3nmpC 3nmvC 3kb3S 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 20096.600 Da / Num. of mol.: 1 / Mutation: A93F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL2, RCAR14, At2g26040, T19L18.15 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O80992 |
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#2: Protein | Mass: 37826.340 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: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9CAJ0, protein-serine/threonine phosphatase |
-Non-polymers , 4 types, 133 molecules
#3: Chemical | ChemComp-PYV / | ||||
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#4: Chemical | #5: Chemical | #6: 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: 51.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M ammonium sulphate, 0.1M Tris, 10% ethyl glycol, 23% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
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: 2.55→30 Å / Num. obs: 19661 / % possible obs: 80.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.4 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 15.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KB3 Resolution: 2.56→29.85 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.907 / SU B: 24.462 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R Free: 0.322 / 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: 41.514 Å2
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Refinement step | Cycle: LAST / Resolution: 2.56→29.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.56→2.626 Å / Total num. of bins used: 20
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