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Yorodumi- PDB-5mgk: Crystal Structure of BAZ2A bromodomain in complex with 4-propiony... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mgk | ||||||
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Title | Crystal Structure of BAZ2A bromodomain in complex with 4-propionyl-pyrrole derivative 2 | ||||||
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: 2.301 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 | 5mgk.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mgk.ent.gz | 43.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/5mgk ftp://data.pdbj.org/pub/pdb/validation_reports/mg/5mgk | HTTPS FTP |
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-Related structure data
Related structure data | 5mgeC 5mgfC 5mggC 5mgjC 5mglC 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 on special symmetry positions |
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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-7MW / |
#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: 3.49 Å3/Da / Density % sol: 64.71 % / Mosaicity: 0.18 ° |
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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: 2.3→47.62 Å / Num. obs: 7850 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 31.74 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.061 / Rrim(I) all: 0.2 / Net I/σ(I): 11 / Num. measured all: 85087 | ||||||||||||||||||
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: 2.301→31.174 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.54 Å2 / Biso mean: 46.1754 Å2 / Biso min: 20.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.301→31.174 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: 3 / % 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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