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- PDB-6i68: Co-crystal structure of human SPOP MATH domain (M117V) and human ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i68 | ||||||
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Title | Co-crystal structure of human SPOP MATH domain (M117V) and human BRD3 fragment | ||||||
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![]() | LIGASE / ligase nuclear cancer ubiquitination | ||||||
Function / homology | ![]() regulation of proteolysis / lncRNA binding / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / endodermal cell differentiation / localization / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding ...regulation of proteolysis / lncRNA binding / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / endodermal cell differentiation / localization / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / chromatin remodeling / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ostertag, M.S. / Popowicz, G.M. / Sattler, M. | ||||||
![]() | ![]() Title: Structural Insights into BET Client Recognition of Endometrial and Prostate Cancer-Associated SPOP Mutants. Authors: Ostertag, M.S. / Hutwelker, W. / Plettenburg, O. / Sattler, M. / Popowicz, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 258.3 KB | Display | ![]() |
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PDB format | ![]() | 209.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.8 KB | Display | ![]() |
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Full document | ![]() | 479.4 KB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i41C ![]() 6i5pC ![]() 6i7aC ![]() 3ivvS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16584.072 Da / Num. of mol.: 4 / Mutation: M117V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 935.995 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 200 mM Sodium formate, 100 mM Bis Tris propane pH 7.5, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 23, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→90.13 Å / Num. obs: 70332 / % possible obs: 99.2 % / Redundancy: 3.07 % / Rrim(I) all: 0.054 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.75→4.75 Å / Num. unique obs: 3410 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IVV Resolution: 1.85→19.868 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.34 / Phase error: 26.76
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→19.868 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: 23.2426 Å / Origin y: -13.0866 Å / Origin z: 66.957 Å
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Refinement TLS group | Selection details: all |