[English] 日本語
![](img/lk-miru.gif)
- PDB-6fh6: Crystal Structure of BAZ2B bromodomain in complex with 1-methylpy... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6fh6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of BAZ2B bromodomain in complex with 1-methylpyridinone compound 1 | ||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
![]() | TRANSCRIPTION / four helical bundle | ||||||
Function / homology | ![]() chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Dalle Vedove, A. / Spiliotopoulos, D. / Lolli, G. / Caflisch, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains. Authors: Dalle Vedove, A. / Spiliotopoulos, D. / D'Agostino, V.G. / Marchand, J.R. / Unzue, A. / Nevado, C. / Lolli, G. / Caflisch, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 39.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 436.2 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fg6C ![]() 6fgfC ![]() 6fggC ![]() 6fghC ![]() 6fgiC ![]() 6fglC ![]() 6fgtC ![]() 6fguC ![]() 6fgvC ![]() 6fgwC ![]() 6fh7C ![]() 4ir5S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13618.652 Da / Num. of mol.: 1 / Fragment: Bromodomain (residues 2054-2168) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-D8Q / ~{ |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.67 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG500MME, 2% PEG1000, 2% PEG3350, 10% PEG20000, 2% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.082→47.999 Å / Num. obs: 8432 / % possible obs: 61.9 % / Redundancy: 7.4 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.082→2.152 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 420 / CC1/2: 0.966 / Rpim(I) all: 0.175 / Rrim(I) all: 0.496 / % possible all: 33.5 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4IR5 Resolution: 2.082→47.998 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.03
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.31 Å2 / Biso mean: 31.8278 Å2 / Biso min: 14.67 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.082→47.998 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
|