[English] 日本語
Yorodumi- PDB-6fap: Crystal structure of human BAZ2A PHD zinc finger in complex with Fr23 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fap | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human BAZ2A PHD zinc finger in complex with Fr23 | ||||||
Components | Bromodomain adjacent to zinc finger domain protein 2A | ||||||
Keywords | TRANSCRIPTION | ||||||
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 / Resolution: 2.7 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fap.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fap.ent.gz | 75.4 KB | Display | PDB format |
PDBx/mmJSON format | 6fap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/6fap ftp://data.pdbj.org/pub/pdb/validation_reports/fa/6fap | HTTPS FTP |
---|
-Related structure data
Related structure data | 6fhqC 6fhuC 6fi0C 6fi1C 6fkpC 4qf2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-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 |
---|
-Non-polymers , 5 types, 40 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.81 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4 M sodium/ potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 2.7→45.73 Å / Num. obs: 7841 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.99 / Rmerge(I) obs: 0.148 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 995 / CC1/2: 0.95 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4qf2 Resolution: 2.7→45.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.944 / SU B: 18.772 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R: 0.881 / ESU R Free: 0.324 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.721 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.7→45.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|