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Yorodumi- PDB-4up5: Crystal structure of the Pygo2 PHD finger in complex with the B9L... -
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-Basic information
Entry | Database: PDB / ID: 4up5 | ||||||
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Title | Crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and a chemical fragment | ||||||
Components | PYGOPUS HOMOLOG 2, B-CELL CLL/LYMPHOMA 9-LIKE PROTEIN | ||||||
Keywords | TRANSCRIPTION / PYGO / WNT SIGNALLING / HISTONE H3 / FRAGMENT SCREENING | ||||||
Function / homology | Function and homology information histone acetyltransferase regulator activity / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / beta-catenin-TCF complex / mammary gland development / regulation of cell morphogenesis / myoblast differentiation / lens development in camera-type eye / roof of mouth development / skeletal muscle cell differentiation ...histone acetyltransferase regulator activity / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / beta-catenin-TCF complex / mammary gland development / regulation of cell morphogenesis / myoblast differentiation / lens development in camera-type eye / roof of mouth development / skeletal muscle cell differentiation / somatic stem cell population maintenance / developmental growth / canonical Wnt signaling pathway / positive regulation of epithelial to mesenchymal transition / kidney development / Deactivation of the beta-catenin transactivating complex / negative regulation of transforming growth factor beta receptor signaling pathway / Formation of the beta-catenin:TCF transactivating complex / brain development / fibrillar center / beta-catenin binding / histone binding / transcription by RNA polymerase II / transcription coactivator activity / chromatin binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Miller, T.C.R. / Fiedler, M. / Rutherford, T.J. / Birchall, K. / Chugh, J. / Bienz, M. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Competitive Binding of a Benzimidazole to the Histone-Binding Pocket of the Pygo Phd Finger. Authors: Miller, T.C.R. / Rutherford, T.J. / Birchall, K. / Chugh, J. / Fiedler, M. / Bienz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4up5.cif.gz | 31.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4up5.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 4up5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4up5 ftp://data.pdbj.org/pub/pdb/validation_reports/up/4up5 | HTTPS FTP |
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-Related structure data
Related structure data | 4up0C 2xb1S 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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Unit cell |
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-Components
#1: Protein | Mass: 10537.676 Da / Num. of mol.: 1 / Fragment: PHD FINGER, HD1,RESIDUES 327-387,240-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: Q9BRQ0, UniProt: Q86UU0 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-94W / | #4: Water | ChemComp-HOH / | Sequence details | GLYCINE (REMNANT OF TEV CLEAVAGE SITE), PYGO2 PHD FINGER ( AAS 327-387), ARTIFICIAL LINKER (8AA ...GLYCINE (REMNANT OF TEV CLEAVAGE SITE), PYGO2 PHD FINGER ( AAS 327-387), ARTIFICIAL | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.81 % / Description: NONE |
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Crystal grow | Details: 60% TACSIMATE, PH 7. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0332 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→31.95 Å / Num. obs: 10894 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XB1 Resolution: 1.65→39.52 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.86 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A RESIDUES 383-387 AND 8AA GSGSGSGS LINKER ARE DISORDERED CHAIN B RESIDUE 263 IS DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.805 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→39.52 Å
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