+Open data
-Basic information
Entry | Database: PDB / ID: 5fta | ||||||||||||
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Title | Crystal structure of the N-terminal BTB domain of human KCTD10 | ||||||||||||
Components | BTB/POZ DOMAIN-CONTAINING ADAPTER FOR CUL3-MEDIATED RHOA DEGRADATION PROTEIN 3 | ||||||||||||
Keywords | TRANSFERASE | ||||||||||||
Function / homology | Function and homology information Notch binding / negative regulation of Rho protein signal transduction / Cul3-RING ubiquitin ligase complex / protein homooligomerization / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / nucleoplasm / identical protein binding / cytosol Similarity search - Function | ||||||||||||
Biological species | HOMO SAPIENS (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å | ||||||||||||
Authors | Pinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Tallant, C. / Newman, J.A. / Kopec, J. / Fitzpatrick, F. / Talon, R. / Collins, P. ...Pinkas, D.M. / Sanvitale, C.E. / Solcan, N. / Goubin, S. / Tallant, C. / Newman, J.A. / Kopec, J. / Fitzpatrick, F. / Talon, R. / Collins, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A. | ||||||||||||
Citation | Journal: Biochem. J. / Year: 2017 Title: Structural complexity in the KCTD family of Cullin3-dependent E3 ubiquitin ligases. Authors: Pinkas, D.M. / Sanvitale, C.E. / Bufton, J.C. / Sorrell, F.J. / Solcan, N. / Chalk, R. / Doutch, J. / Bullock, A.N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fta.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fta.ent.gz | 125.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fta.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/5fta ftp://data.pdbj.org/pub/pdb/validation_reports/ft/5fta | HTTPS FTP |
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-Related 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: 12600.397 Da / Num. of mol.: 4 / Fragment: BTB DOMAIN, UNP RESIDUES 26-135 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9H3F6 #2: Chemical | ChemComp-HG / #3: 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: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 8.4 Details: 20% PEG3350, 0.1M TRIS PH 8.4, 0.2M MAGNESIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→17.77 Å / Num. obs: 13630 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.64→2.71 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.4 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.64→17.766 Å / SU ML: 0.36 / σ(F): 1.37 / Phase error: 28.66 / 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: 2.64→17.766 Å
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Refine LS restraints |
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LS refinement shell |
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