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- PDB-5mgm: Crystal Structure of BAZ2A bromodomain in complex with acetopheno... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mgm | ||||||
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Title | Crystal Structure of BAZ2A bromodomain in complex with acetophenone derivative 4 | ||||||
![]() | 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. / Spiliotopoulos, D. / Caflisch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery of BAZ2A bromodomain ligands. Authors: Spiliotopoulos, D. / Wamhoff, E.C. / Lolli, G. / Rademacher, C. / 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 | ![]() | 35.2 KB | Display | ![]() |
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PDB format | ![]() | 22 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.2 KB | Display | ![]() |
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Full document | ![]() | 423.2 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mgeC ![]() 5mgfC ![]() 5mggC ![]() 5mgjC ![]() 5mgkC ![]() 5mglC ![]() 4lz2S C: citing same article ( S: Starting model for refinement |
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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, UNP residues 1796-1898 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-7MZ / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.2 % / Mosaicity: 1 ° |
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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: Oct 5, 2016 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.8→27.38 Å / Num. obs: 4298 / % possible obs: 99.5 % / Redundancy: 9.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.318 / Net I/σ(I): 7.1 | ||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LZ2 Resolution: 2.8→27.38 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.879 / SU B: 10.97 / SU ML: 0.211 / SU R Cruickshank DPI: 0.154 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.07
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.01 Å2 / Biso mean: 41.931 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 2.8→27.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Total num. of bins used: 20
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