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Yorodumi- PDB-6f8g: Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f8g | ||||||
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Title | Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment | ||||||
Components |
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Keywords | LIGASE / Nuclear / Diabetes | ||||||
Function / homology | Function and homology information regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / positive regulation of insulin secretion / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / positive regulation of insulin secretion / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / ubiquitin protein ligase binding / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mesocricetus auratus (golden hamster) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Ostertag, M.S. / Popowicz, G.M. / Sattler, M. | ||||||
Citation | Journal: Structure / Year: 2019 Title: The Structure of the SPOP-Pdx1 Interface Reveals Insights into the Phosphorylation-Dependent Binding Regulation. Authors: Ostertag, M.S. / Messias, A.C. / Sattler, M. / Popowicz, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f8g.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f8g.ent.gz | 107.2 KB | Display | PDB format |
PDBx/mmJSON format | 6f8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/6f8g ftp://data.pdbj.org/pub/pdb/validation_reports/f8/6f8g | HTTPS FTP |
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-Related structure data
Related structure data | 6f8fC 3ivvS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 16616.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791 #2: Protein/peptide | Mass: 1248.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mesocricetus auratus (golden hamster) / References: UniProt: P70118 #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: 2.03 Å3/Da / Density % sol: 39.47 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→100 Å / Num. all: 124076 / Num. obs: 32906 / % possible obs: 96.4 % / Redundancy: 3.54 % / Rrim(I) all: 0.106 / Net I/σ(I): 8.62 |
Reflection shell | Resolution: 2.05→2.102 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IVV Resolution: 2.03→19.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.358 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.798 Å2
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Refinement step | Cycle: 1 / Resolution: 2.03→19.85 Å
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Refine LS restraints |
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