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Yorodumi- PDB-6fhq: Crystal structure of human BAZ2B PHD zinc finger in complex with Fr 21 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fhq | ||||||
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Title | Crystal structure of human BAZ2B PHD zinc finger in complex with Fr 21 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
Keywords | TRANSCRIPTION / PHD / zinc finger / BAZ2B / BAZ2A / bromodomain / fragment / competition / epigenetic | ||||||
Function / homology | Function and homology information chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 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 | 6fhq.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fhq.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fhq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fhq_validation.pdf.gz | 438.8 KB | Display | wwPDB validaton report |
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Full document | 6fhq_full_validation.pdf.gz | 438.8 KB | Display | |
Data in XML | 6fhq_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 6fhq_validation.cif.gz | 9.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/6fhq ftp://data.pdbj.org/pub/pdb/validation_reports/fh/6fhq | HTTPS FTP |
-Related structure data
Related structure data | 6fapC 6fhuC 6fi0C 6fi1C 6fkpC 4qf3S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6543.708 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BAZ2B, KIAA1476 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UIF8 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-DE5 / | #4: 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: 2.19 Å3/Da / Density % sol: 43.79 % |
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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: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→65.04 Å / Num. obs: 8453 / % possible obs: 97.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.95→2 Å / Num. unique obs: 527 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 4QF3 Resolution: 1.95→37.24 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.545 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.166 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.102 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→37.24 Å
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Refine LS restraints |
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