+Open data
-Basic information
Entry | Database: PDB / ID: 6fi0 | ||||||
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Title | Crystal structure of BAZ2A PHD zinc finger in complex with Fr 19 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2A | ||||||
Keywords | TRANSCRIPTION / PHD zinc finger / bromodomain / BAZ2A / fragment / Fr 19 / Fr19 / epigenetic / ligandability | ||||||
Function / homology | Function and homology information NoRC complex / : / : / rDNA heterochromatin / : / rDNA heterochromatin formation / : / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I ...NoRC complex / : / : / rDNA heterochromatin / : / rDNA heterochromatin formation / : / chromatin silencing complex / RNA polymerase I preinitiation complex assembly / negative regulation of transcription by RNA polymerase I / heterochromatin formation / nuclear receptor binding / lysine-acetylated histone binding / NoRC negatively regulates rRNA expression / histone binding / nuclear speck / chromatin remodeling / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / RNA binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Amato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A. | ||||||
Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach. Authors: Amato, A. / Lucas, X. / Bortoluzzi, A. / Wright, D. / Ciulli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fi0.cif.gz | 101.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fi0.ent.gz | 78.5 KB | Display | PDB format |
PDBx/mmJSON format | 6fi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/6fi0 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/6fi0 | HTTPS FTP |
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-Related structure data
Related structure data | 6fapC 6fhqC 6fhuC 6fi1C 6fkpC 4qf2S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 6597.694 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2A, KIAA0314, TIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF9 |
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-Non-polymers , 6 types, 178 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.2-2.4 M sodium/potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→45.34 Å / Num. obs: 21069 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.9→1.94 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QF2 Resolution: 1.9→45.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.36 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.775 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→45.34 Å
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Refine LS restraints |
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