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Open data
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Basic information
Entry | Database: PDB / ID: 7bl8 | |||||||||
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Title | BAZ2A bromodomain in complex with the chemical probe BAZ2-ICR | |||||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2A | |||||||||
![]() | TRANSCRIPTION / four helical bundle | |||||||||
Function / homology | ![]() 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 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 / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / nucleus / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Dalle Vedove, A. / Cazzanelli, G. / Caflisch, A. / Lolli, G. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.5 KB | Display | ![]() |
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PDB format | ![]() | 23.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 849.8 KB | Display | ![]() |
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Full document | ![]() | 850 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bl9C ![]() 7blaC ![]() 7blbC ![]() 7blcC ![]() 7bldC ![]() 5mgjS 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
#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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-U1Z / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.68 % / Mosaicity: 0 ° |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 15, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→47.66 Å / Num. obs: 6016 / % possible obs: 98.8 % / Redundancy: 3.4 % / CC1/2: 0.988 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.068 / Rrim(I) all: 0.129 / Net I/σ(I): 7.7 / Num. measured all: 20276 / Scaling rejects: 42 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MGJ Resolution: 2.5→47.658 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 27.95 / 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: 94.41 Å2 / Biso mean: 42.0619 Å2 / Biso min: 15.09 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→47.658 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: 98 %
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