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- PDB-6i41: Co-crystal structure of human SPOP MATH domain (wild-type) and hu... -
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Basic information
Entry | Database: PDB / ID: 6i41 | ||||||
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Title | Co-crystal structure of human SPOP MATH domain (wild-type) 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 / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding / protein polyubiquitination ...regulation of proteolysis / lncRNA binding / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / Hedgehog 'on' state / lysine-acetylated histone binding / protein polyubiquitination / chromatin organization / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / 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 | ![]() | 76.2 KB | Display | ![]() |
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PDB format | ![]() | 55.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6i5pC ![]() 6i68C ![]() 6i7aC ![]() 3ivvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16616.137 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminus of protein could not be completely modeled in X-ray data. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 935.995 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminus of polypeptide could not be completely modeled from electron density in X-ray data. Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.28 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100 mM Tris pH 8.5, 200 mM NaCl, 25% (w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 24, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→40.8 Å / Num. obs: 13067 / % possible obs: 98.3 % / Redundancy: 6.5 % / Rrim(I) all: 0.058 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.79→1.82 Å / Num. unique obs: 534 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3IVV Resolution: 1.9→19.632 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.52 / Phase error: 30.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.632 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: -13.8177 Å / Origin y: 0.2796 Å / Origin z: -4.5573 Å
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Refinement TLS group | Selection details: all |