+Open data
-Basic information
Entry | Database: PDB / ID: 5o75 | |||||||||
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Title | Ube4B U-box domain | |||||||||
Components | Ubiquitin conjugation factor E4 B | |||||||||
Keywords | LIGASE / E3 U-box / ubiquitin transfer | |||||||||
Function / homology | Function and homology information granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / ubiquitin ligase complex / response to UV / : / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding ...granzyme-mediated apoptotic signaling pathway / ubiquitin-ubiquitin ligase activity / ubiquitin ligase complex / response to UV / : / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / enzyme binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.483 Å | |||||||||
Authors | Gabrielsen, M. / Buetow, L. / Nakasone, M.A. / Huang, D.T. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Mol. Cell / Year: 2017 Title: A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants. Authors: Gabrielsen, M. / Buetow, L. / Nakasone, M.A. / Ahmed, S.F. / Sibbet, G.J. / Smith, B.O. / Zhang, W. / Sidhu, S.S. / Huang, D.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o75.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o75.ent.gz | 32.8 KB | Display | PDB format |
PDBx/mmJSON format | 5o75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o75 ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o75 | HTTPS FTP |
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-Related structure data
Related structure data | 5o6sC 5o6tC 5o76C 3l1zS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 9014.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE4B, HDNB1, KIAA0684, UFD2 / Plasmid: pGEX4T.1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O95155, RING-type E3 ubiquitin transferase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M citric acid, pH 5.5, 1.9 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97628 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97628 Å / Relative weight: 1 |
Reflection | Resolution: 1.483→69.438 Å / Num. obs: 11868 / % possible obs: 91.9 % / Redundancy: 17 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.015 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.483→1.509 Å / Redundancy: 15 % / Rmerge(I) obs: 1.194 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 636 / CC1/2: 0.771 / Rpim(I) all: 0.435 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L1Z Resolution: 1.483→40.09 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.46 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.483→40.09 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.0621 Å / Origin y: 41.9737 Å / Origin z: 88.9428 Å
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Refinement TLS group | Selection details: all |