+Open data
-Basic information
Entry | Database: PDB / ID: 6jx5 | |||||||||
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Title | Hect domain of AREL1 | |||||||||
Components | Apoptosis-resistant E3 ubiquitin protein ligase 1 | |||||||||
Keywords | APOPTOSIS / HECT domain | |||||||||
Function / homology | Function and homology information protein K33-linked ubiquitination / protein K11-linked ubiquitination / HECT-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process ...protein K33-linked ubiquitination / protein K11-linked ubiquitination / HECT-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / apoptotic process / negative regulation of apoptotic process / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å | |||||||||
Authors | Sivaraman, J. / Singh, S. / Ng, J. / Nayak, D. | |||||||||
Funding support | Singapore, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural insights into a HECT-type E3 ligase AREL1 and its ubiquitination activitiesin vitro. Authors: Singh, S. / Ng, J. / Nayak, D. / Sivaraman, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jx5.cif.gz | 241 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jx5.ent.gz | 193.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jx5_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
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Full document | 6jx5_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 6jx5_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 6jx5_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/6jx5 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/6jx5 | HTTPS FTP |
-Related structure data
Related structure data | 6jx6C 3tugS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 44542.734 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AREL1, KIAA0317 / Production host: Escherichia coli (E. coli) References: UniProt: O15033, HECT-type E3 ubiquitin transferase #2: Water | ChemComp-HOH / | |
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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: 3.93 Å3/Da / Density % sol: 68.74 % |
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Crystal grow | Temperature: 296.15 K / Method: vapor diffusion / Details: 100mM Bis Tris (pH 5.5), 200mM Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 296 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9926 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9926 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.86 Å / Num. obs: 77372 / % possible obs: 98.65 % / Redundancy: 5.7 % / Biso Wilson estimate: 36.23 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.049 / Net I/σ(I): 19.22 |
Reflection shell | Resolution: 2.402→2.488 Å / Num. unique obs: 7296 / CC1/2: 0.832 / Rpim(I) all: 0.235 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TUG Resolution: 2.402→47.86 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.402→47.86 Å
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Refine LS restraints |
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LS refinement shell |
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