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Yorodumi- PDB-5mgl: Crystal Structure of BAZ2A bromodomain in complex with 4-chloropy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mgl | ||||||
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Title | Crystal Structure of BAZ2A bromodomain in complex with 4-chloropyridine derivative 3 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2A | ||||||
Keywords | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.651 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 | 5mgl.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mgl.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 5mgl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mgl ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mgl | HTTPS FTP |
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-Related structure data
Related structure data | 5mgeC 5mgfC 5mggC 5mgjC 5mgkC 5mgmC 4lz2S 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: 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.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UIF9 |
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#2: Chemical | ChemComp-7MU / |
#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: 3.5 Å3/Da / Density % sol: 64.81 % |
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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: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å | ||||||||||||||||||
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: 2.65→27.063 Å / Num. obs: 5180 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.979 / Rmerge(I) obs: 0.268 / Net I/σ(I): 7 | ||||||||||||||||||
Reflection shell |
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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: 4LZ2 Resolution: 2.651→27.063 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.14 Å2 / Biso mean: 35.1772 Å2 / Biso min: 10 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.651→27.063 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: 2 / % reflection obs: 100 %
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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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