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Open data
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Basic information
Entry | Database: PDB / ID: 3kdj | ||||||
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Title | Complex structure of (+)-ABA-bound PYL1 and ABI1 | ||||||
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![]() | HYDROLASE/Hormone Receptor / ABA / PYL1 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() regulation of abscisic acid-activated signaling pathway / negative regulation of abscisic acid-activated signaling pathway / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yin, P. / Fan, H. / Hao, Q. / Yuan, X. / Yan, N. | ||||||
![]() | ![]() Title: Structural insights into the mechanism of abscisic acid signaling by PYL proteins Authors: Yin, P. / Fan, H. / Hao, Q. / Yuan, X. / Wu, D. / Pang, Y. / Yan, C. / Li, W. / Wang, J. / Yan, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 199.5 KB | Display | ![]() |
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PDB format | ![]() | 157.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3kdhSC ![]() 3kdiC ![]() 2p8eS S: Starting model for refinement C: citing same article ( |
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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: 23327.898 Da / Num. of mol.: 1 / Fragment: residues 20-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 34792.836 Da / Num. of mol.: 1 / Fragment: residues 119-434 / Mutation: C208S, D378G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P49597, protein-serine/threonine phosphatase |
#3: Chemical | ChemComp-A8S / (![]() |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M citric acid pH 5.5, 0.01M GSH/GSSG, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.878→34.15 Å / Num. obs: 44478 / % possible obs: 90.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 34.99 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.75 |
Reflection shell | Resolution: 1.878→1.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.87 / Num. unique all: 2581 / % possible all: 53.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRIES: 3KDH and 2P8E Resolution: 1.878→34.15 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.718 / SU ML: 0.28 / Isotropic thermal model: TLS / σ(F): 1.34 / Phase error: 33.13 / 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 / Bsol: 59.253 Å2 / ksol: 0.345 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 260.35 Å2 / Biso mean: 60.477 Å2 / Biso min: 30.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.878→34.15 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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