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Open data
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Basic information
Entry | Database: PDB / ID: 9gnl | ||||||
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Title | X-ray crystal structure of VvPYL1 with ABA | ||||||
![]() | Abscisic acid receptor PYR1 | ||||||
![]() | PLANT PROTEIN / VvPYL1 / ABA receptor protein | ||||||
Function / homology | ![]() abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rivera-Moreno, M. / Benavente, J.L. / Infantes, L. / Albert, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Regulation of transpiration in grapevine through chemical activation of ABA signaling by ABA receptor agonists Authors: Rivera-Moreno, M. / Benavente, J.L. / Infantes, L. / Albert, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.7 KB | Display | ![]() |
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PDB format | ![]() | 132.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 882.8 KB | Display | ![]() |
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Full document | ![]() | 900.3 KB | Display | |
Data in XML | ![]() | 20.3 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9gnmC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.930106578665, 0.351876790046, 0.105282842621), (0.365418849894, 0.857641183721, 0.361829606483), (0.0370245387021, 0.37501243261, -0.926280119036)Vector: -5. ...NCS oper: (Code: given Matrix: (-0.930106578665, 0.351876790046, 0.105282842621), Vector: |
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Components
#1: Protein | Mass: 24045.748 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: F6HT94 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M sodium acetate, pH 5.0, 0.2 M magnesium chloride, 20% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2023 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972422 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→46.83 Å / Num. obs: 47169 / % possible obs: 98.25 % / Redundancy: 3.3 % / Biso Wilson estimate: 57.76 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.102 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.4→2.489 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 14366 / CC1/2: 0.62 / Rpim(I) all: 0.922 / % possible all: 96.83 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→46.83 Å
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 1.25004845257 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -1.80614616923 Å / Origin y: 3.56783535208 Å / Origin z: 17.3710055238 Å
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Refinement TLS group | Selection details: all |