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Yorodumi- PDB-5mge: Crystal structure of BAZ2B bromodomain in complex with 1-methylpy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mge | ||||||
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Title | Crystal structure of BAZ2B bromodomain in complex with 1-methylpyridine derivative 1 | ||||||
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: 1.95 Å | ||||||
Authors | Lolli, G. / Spiliotopoulos, D. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Eur J Med Chem / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mge.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mge.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mge ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mge | HTTPS FTP |
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-Related structure data
Related structure data | 5mgfC 5mggC 5mgjC 5mgkC 5mglC 5mgmC 4ir5S S: Starting model for refinement C: citing same article (ref.) |
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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: 13531.574 Da / Num. of mol.: 1 / Fragment: Bromodomain, UNP residues 2054-2167 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-7MX / |
#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: 4.14 Å3/Da / Density % sol: 70.31 % / Mosaicity: 0.26 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG500MME (20%), PEG1000 (2%), PEG3350 (2%), PEG20000 (10%), MPD (2%) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→48.38 Å / Num. obs: 16759 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-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: 1.95→48.376 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.74
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.23 Å2 / Biso mean: 42.1416 Å2 / Biso min: 19.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→48.376 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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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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