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Yorodumi- PDB-6fh7: Crystal Structure of BAZ2B bromodomain in complex with 1-methylpy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fh7 | ||||||
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Title | Crystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 2 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | Function and homology information chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Dalle Vedove, A. / Spiliotopoulos, D. / Lolli, G. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: ChemMedChem / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fh7.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fh7.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 6fh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/6fh7 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/6fh7 | HTTPS FTP |
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-Related structure data
Related structure data | 6fg6C 6fgfC 6fggC 6fghC 6fgiC 6fglC 6fgtC 6fguC 6fgvC 6fgwC 6fh6C 4ir5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13618.652 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168) Source method: isolated from a genetically manipulated source Details: First two residues SM derive from the expression tag Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF8 |
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#2: Chemical | ChemComp-EN2 / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.2 Å / Num. obs: 9692 / % possible obs: 72.4 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.391 / Num. unique obs: 484 / CC1/2: 0.958 / Rpim(I) all: 0.156 / Rrim(I) all: 0.439 / % possible all: 42.5 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IR5 Resolution: 2.1→48.197 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.44
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.08 Å2 / Biso mean: 36.3876 Å2 / Biso min: 17.77 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→48.197 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: 4
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