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Yorodumi- PDB-6fgt: Crystal Structure of BAZ2B bromodomain in complex with 1-methylpy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fgt | ||||||
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Title | Crystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 3 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | Function and homology information chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Dalle Vedove, A. / Spiliotopoulos, D. / Lolli, G. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: ChemMedChem / Year: 2018 Title: Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains. Authors: Dalle Vedove, A. / Spiliotopoulos, D. / D'Agostino, V.G. / Marchand, J.R. / Unzue, A. / Nevado, C. / Lolli, G. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fgt.cif.gz | 40.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fgt.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 6fgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fgt_validation.pdf.gz | 940.8 KB | Display | wwPDB validaton report |
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Full document | 6fgt_full_validation.pdf.gz | 943.3 KB | Display | |
Data in XML | 6fgt_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 6fgt_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/6fgt ftp://data.pdbj.org/pub/pdb/validation_reports/fg/6fgt | HTTPS FTP |
-Related structure data
Related structure data | 6fg6C 6fgfC 6fggC 6fghC 6fgiC 6fglC 6fguC 6fgvC 6fgwC 6fh6C 6fh7C 5dyuS 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: 13618.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8 |
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#2: Chemical | ChemComp-D9T / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.34 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 5, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.29 Å / Num. obs: 15653 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.024 / Rrim(I) all: 0.066 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1148 / CC1/2: 0.983 / Rpim(I) all: 0.162 / Rrim(I) all: 0.451 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DYU Resolution: 2→40.803 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 34.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40.803 Å
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Refine LS restraints |
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LS refinement shell |
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