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- PDB-4ir5: Crystal Structure of the bromodomain of human BAZ2B in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ir5 | ||||||
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Title | Crystal Structure of the bromodomain of human BAZ2B in complex with 1-{1-[2-(hydroxymethyl)phenyl]-7-phenoxyindolizin-3-yl}ethanone (GSK2847449A) | ||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
![]() | TRANSCRIPTION / SGC / Structural Genomics Consortium / bromodomain / acetylated lysine binding protein / KIAA1476 / WALp4 | ||||||
Function / homology | ![]() chromatin remodeling / regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chaikuad, A. / Felletar, I. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. ...Chaikuad, A. / Felletar, I. / Chung, C.W. / Drewry, D. / Chen, P. / Filippakopoulos, P. / Fedorov, O. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Discovery and Characterization of GSK2801, a Selective Chemical Probe for the Bromodomains BAZ2A and BAZ2B. Authors: Chen, P. / Chaikuad, A. / Bamborough, P. / Bantscheff, M. / Bountra, C. / Chung, C.W. / Fedorov, O. / Grandi, P. / Jung, D. / Lesniak, R. / Lindon, M. / Muller, S. / Philpott, M. / Prinjha, ...Authors: Chen, P. / Chaikuad, A. / Bamborough, P. / Bantscheff, M. / Bountra, C. / Chung, C.W. / Fedorov, O. / Grandi, P. / Jung, D. / Lesniak, R. / Lindon, M. / Muller, S. / Philpott, M. / Prinjha, R. / Rogers, C. / Selenski, C. / Tallant, C. / Werner, T. / Willson, T.M. / Knapp, S. / Drewry, D.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.9 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 816.7 KB | Display | ![]() |
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Full document | ![]() | 817.3 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ir3C ![]() 4ir4C ![]() 4ir6C ![]() 4rvrC ![]() 3g0lS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IR5 / | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IN THIS ENTRY CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.19 Å3/Da / Density % sol: 70.63 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 28% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.5 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution), VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 4, 2011 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.48 Å / Num. all: 25305 / Num. obs: 25280 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 5 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3598 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3G0L Resolution: 1.7→27.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.585 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.078 / ESU R Free: 0.086 / 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: 30.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.209 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→27.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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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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