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- PDB-8j4b: Crystal structure of OY phytoplasma SAP05 in complex with AtSPL13 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8j4b | |||||||||||||||
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Title | Crystal structure of OY phytoplasma SAP05 in complex with AtSPL13 | |||||||||||||||
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![]() | PLANT PROTEIN / ubiquitin-independent protein degradation | |||||||||||||||
Function / homology | ![]() anther development / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Dong, C. / Yan, X. / Yuan, X. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of SAP05-mediated ubiquitin-independent proteasomal degradation of transcription factors. Authors: Yan, X. / Yuan, X. / Lv, J. / Zhang, B. / Huang, Y. / Li, Q. / Ma, J. / Li, Y. / Wang, X. / Li, Y. / Yu, Y. / Liu, Q. / Liu, T. / Mi, W. / Dong, C. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j48C ![]() 8j49C ![]() 8j4aC 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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Components
#1: Protein | Mass: 12288.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: OY-M / Gene: PAM_518 / Production host: ![]() ![]() #2: Protein | Mass: 7686.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2828 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.93 Å / Num. obs: 27306 / % possible obs: 99.5 % / Redundancy: 9.1 % / Biso Wilson estimate: 26.88 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.74 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 3.21 / Num. unique obs: 2608 / CC1/2: 0.627 |
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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 | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→36.93 Å
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Refine LS restraints |
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LS refinement shell |
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