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Open data
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Basic information
Entry | Database: PDB / ID: 7xwf | ||||||||||||
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Title | RLGSGG-AtPRT6 UBR box (highest resolution) | ||||||||||||
![]() | E3 ubiquitin-protein ligase PRT6 | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kim, L. / Song, H.K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analyses of plant PRT6-UBR box for Cys-Arg/N-degron pathway and insights into the plant submergence resistance Authors: Kim, L. / Lin, C.C. / Lin, T.J. / Cao, Y.C. / Chen, M.C. / Chou, M.Y. / Lin, W.H. / Kim, M. / Wu, J.L. / Shih, M.C. / Song, H.K. / Ho, M.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 | ![]() | 38.9 KB | Display | ![]() |
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PDB format | ![]() | 24.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xwdC ![]() 7xweC ![]() 7xwgC ![]() 7y6wC ![]() 7y6xC ![]() 7y6yC ![]() 7y6zC ![]() 7y70C ![]() 6lhnS S: Starting model for refinement 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8132.913 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: PRT6, CER3, GED1, At5g02310/At5g02300, T1E22.70/T1E22.60 Production host: ![]() ![]() ![]() References: UniProt: F4KCC2, RING-type E3 ubiquitin transferase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.35 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium acetate hydrate, 17 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.451→36.06 Å / Num. obs: 13083 / % possible obs: 90.47 % / Redundancy: 7.7 % / CC1/2: 0.999 / Net I/σ(I): 28.86 |
Reflection shell | Resolution: 1.451→1.503 Å / Num. unique obs: 851 / CC1/2: 0.921 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6LHN Resolution: 1.451→36.06 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.57 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.451→36.06 Å
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Refine LS restraints |
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LS refinement shell |
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