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- PDB-5or8: Crystal Structure of BAZ2A bromodomain in complex with 1,3-dimeth... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5or8 | ||||||
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Title | Crystal Structure of BAZ2A bromodomain in complex with 1,3-dimethyl-benzimidazolone compound 1 | ||||||
![]() | 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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Lolli, G. / Dalle Vedove, A. / Marchand, J.-R. / Caflisch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. Authors: Marchand, J.R. / Dalle Vedove, A. / Lolli, G. / Caflisch, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.9 KB | Display | ![]() |
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PDB format | ![]() | 23.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 683 KB | Display | ![]() |
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Full document | ![]() | 683.7 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5or9C ![]() 5orbC ![]() 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: 12509.048 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP 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-JR4 / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.93 % / Mosaicity: 0.2 ° |
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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 | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
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: 2.4→47.57 Å / Num. obs: 6827 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.258 / Rpim(I) all: 0.086 / Rrim(I) all: 0.272 / Net I/σ(I): 8.3 | ||||||||||||||||||||||||
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→41.195 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 92.06 Å2 / Biso mean: 40.223 Å2 / Biso min: 19.02 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→41.195 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2 / % reflection obs: 100 %
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