+Open data
-Basic information
Entry | Database: PDB / ID: 7y6x | ||||||||||||
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Title | RRGSGG-AtPRT6 UBR box (P32) | ||||||||||||
Components | E3 ubiquitin-protein ligase PRT6 | ||||||||||||
Keywords | LIGASE / PRT6 / UBR box / E3 ubiquitin ligase / Arabidopsis thaliana | ||||||||||||
Function / homology | Function and homology information regulation of seed germination / ubiquitin-dependent protein catabolic process via the N-end rule pathway / regulation of lipid catabolic process / response to abscisic acid / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination ...regulation of seed germination / ubiquitin-dependent protein catabolic process via the N-end rule pathway / regulation of lipid catabolic process / response to abscisic acid / defense response to fungus / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / ubiquitin-dependent protein catabolic process / protein ubiquitination / defense response to bacterium / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.196 Å | ||||||||||||
Authors | Kim, L. / Song, H.K. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y6x.cif.gz | 206.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7y6x.ent.gz | 167.3 KB | Display | PDB format |
PDBx/mmJSON format | 7y6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/7y6x ftp://data.pdbj.org/pub/pdb/validation_reports/y6/7y6x | HTTPS FTP |
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-Related structure data
Related structure data | 7xwdC 7xweC 7xwfC 7xwgC 7y6wC 7y6yC 7y6zC 7y70C 6lhnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 8176.949 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) Gene: PRT6, CER3, GED1, At5g02310/At5g02300, T1E22.70/T1E22.60 Production host: Escherichia coli (E. coli) References: UniProt: F4KCC2, RING-type E3 ubiquitin transferase #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.2 M DL-Malic acid pH 7.0, 0.1 M BIS-Tris pH 7.0 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.196→44.65 Å / Num. obs: 52178 / % possible obs: 97.14 % / Redundancy: 5.5 % / CC1/2: 0.976 / Net I/σ(I): 10.73077 |
Reflection shell | Resolution: 2.196→2.275 Å / Num. unique obs: 4996 / CC1/2: 0.39 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6LHN Resolution: 2.196→44.65 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 24.69 / 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: 2.196→44.65 Å
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Refine LS restraints |
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LS refinement shell |
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