+Open data
-Basic information
Entry | Database: PDB / ID: 7bl9 | |||||||||
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Title | BAZ2A bromodomain in complex with GSK2801 chemical probe | |||||||||
Components | Bromodomain adjacent to zinc finger domain protein 2A | |||||||||
Keywords | TRANSCRIPTION / four helical bundle | |||||||||
Function / homology | Function and homology information NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : ...NoRC complex / : / : / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / : / negative regulation of transcription by RNA polymerase I / : / heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / nucleolus / regulation of DNA-templated transcription / DNA binding / RNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | |||||||||
Authors | Dalle Vedove, A. / Cazzanelli, G. / Caflisch, A. / Lolli, G. | |||||||||
Funding support | Italy, Switzerland, 2items
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Citation | Journal: to be published Title: Chemical probes in the BAZ2A bromodomain Authors: Cazzanelli, G. / Dalle Vedove, A. / D'Agostino, V.G. / Caflisch, A. / Lolli, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bl9.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bl9.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 7bl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7bl9 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7bl9 | HTTPS FTP |
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-Related structure data
Related structure data | 7bl8C 7blaC 7blbC 7blcC 7bldC 5mgjS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12380.919 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 1796-1899) Mutation: First two residues SM derive from the expression tag Source method: isolated from a genetically manipulated source Details: First two residues SM derive from the expression tag Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9 |
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#2: Chemical | ChemComp-3WQ / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.77 % / Mosaicity: 0.11 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2 M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.943 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 20, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.943 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→38.312 Å / Num. obs: 24160 / % possible obs: 100 % / Redundancy: 12.4 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Rrim(I) all: 0.057 / Net I/σ(I): 23 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MGJ Resolution: 1.3→38.31 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.8 Å2 / Biso mean: 26.1174 Å2 / Biso min: 11.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→38.31 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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