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- PDB-7qvu: BAZ2A bromodomain in complex with acetylpyrrole derivative fragment 25 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qvu | ||||||
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Title | BAZ2A bromodomain in complex with acetylpyrrole derivative fragment 25 | ||||||
![]() | 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: Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. Authors: Dalle Vedove, A. / Cazzanelli, G. / Batiste, L. / Marchand, J.R. / Spiliotopoulos, D. / Corsi, J. / 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 | ![]() | 61.6 KB | Display | ![]() |
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PDB format | ![]() | 43.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739.5 KB | Display | ![]() |
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Full document | ![]() | 739.8 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7b7bC ![]() 7b7gC ![]() 7b7iC ![]() 7b82C ![]() 7bc2C ![]() 7qvtC ![]() 7qvvC ![]() 7qwfC ![]() 7qwuC ![]() 7qwyC ![]() 7qx2C ![]() 7qx9C ![]() 7qxlC ![]() 7qyeC ![]() 7qyoC ![]() 7qytC ![]() 7qyuC ![]() 7qyvC ![]() 7qywC ![]() 7qz0C ![]() 7qz4C ![]() 7qzbC ![]() 7qzcC ![]() 7qziC ![]() 7qztC ![]() 7r01C ![]() 7r0bC ![]() 5mgjS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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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 Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FIY / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.29 % / Mosaicity: 0.5 ° |
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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 PILATUS 2M / Detector: PIXEL / Date: Mar 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→47.89 Å / Num. obs: 7041 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.096 / Rrim(I) all: 0.316 / Net I/σ(I): 7.5 / Num. measured all: 75827 | ||||||||||||||||||||||||||||||
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: 2.4→41.47 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.35 / 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: 106.98 Å2 / Biso mean: 41.5066 Å2 / Biso min: 16.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→41.47 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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