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- PDB-6fgv: Crystal Structure of BAZ2A bromodomain in complex with 1-methylpy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fgv | ||||||
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Title | Crystal Structure of BAZ2A bromodomain in complex with 1-methylpyridinone compound 3 | ||||||
![]() | 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 / DNA methylation-dependent heterochromatin formation / negative regulation of transcription by RNA polymerase I / lysine-acetylated histone binding / nuclear receptor binding / NoRC negatively regulates rRNA expression ...NoRC complex / rDNA heterochromatin / rDNA heterochromatin formation / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / DNA methylation-dependent heterochromatin formation / negative regulation of transcription by RNA polymerase I / lysine-acetylated histone binding / nuclear receptor binding / NoRC negatively regulates rRNA expression / heterochromatin formation / histone binding / chromatin remodeling / nuclear speck / 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. / Spiliotopoulos, D. / Lolli, G. / Caflisch, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains. Authors: Dalle Vedove, A. / Spiliotopoulos, D. / D'Agostino, V.G. / Marchand, J.R. / Unzue, A. / Nevado, C. / 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 KB | Display | ![]() |
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PDB format | ![]() | 22.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fg6C ![]() 6fgfC ![]() 6fggC ![]() 6fghC ![]() 6fgiC ![]() 6fglC ![]() 6fgtC ![]() 6fguC ![]() 6fgwC ![]() 6fh6C ![]() 6fh7C ![]() 5mgjS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 12509.048 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-D9T / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.8 % |
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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 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→47.393 Å / Num. obs: 6042 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.035 / Rrim(I) all: 0.112 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 9.2 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 654 / CC1/2: 0.875 / Rpim(I) all: 0.47 / Rrim(I) all: 1.435 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5MGJ Resolution: 2.5→47.393 Å / SU ML: 0.33 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 35.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→47.393 Å
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Refine LS restraints |
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LS refinement shell |
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