+Open data
-Basic information
Entry | Database: PDB / ID: 6lhn | ||||||
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Title | RLGSGG-AtPRT6 UBR box | ||||||
Components | E3 ubiquitin-protein ligase PRT6 | ||||||
Keywords | LIGASE / PRT6 / 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: 2.5 Å | ||||||
Authors | Kim, L. / Kwon, D.H. / Song, H.K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway. Authors: Kim, L. / Kwon, D.H. / Heo, J. / Park, M.R. / Song, H.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lhn.cif.gz | 39.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lhn.ent.gz | 26.2 KB | Display | PDB format |
PDBx/mmJSON format | 6lhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lhn_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6lhn_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6lhn_validation.xml.gz | 4.9 KB | Display | |
Data in CIF | 6lhn_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/6lhn ftp://data.pdbj.org/pub/pdb/validation_reports/lh/6lhn | HTTPS FTP |
-Related structure data
Related structure data | 6kgiC 6kgjC 6khzC 6kgg S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8189.965 Da / Num. of mol.: 1 / Fragment: UBR box 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 | ||
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#2: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.45 Å3/Da / Density % sol: 72.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M ammonium sulfate, 0.1M MES pH6.5 |
-Data collection
Diffraction | Mean temperature: 193 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.499→42.67 Å / Num. obs: 5522 / % possible obs: 99.48 % / Redundancy: 9 % / CC1/2: 0.986 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.5→2.589 Å / Num. unique obs: 5513 / CC1/2: 0.714 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6KGG 6kgg Resolution: 2.5→38.95 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 23.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→38.95 Å
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Refine LS restraints |
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LS refinement shell |
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