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- PDB-4xua: 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: 4xua | ||||||
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Title | Crystal Structure of the bromodomain of human BAZ2B in complex with E11919 BAZ2-ICR analogue | ||||||
![]() | Bromodomain adjacent to zinc finger domain protein 2B | ||||||
![]() | TRANSCRIPTION / bromodomain / acetylated lysine binding protein / KIAA1476 / WALp4 / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
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. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
![]() | ![]() Title: Structure Enabled Design of BAZ2-ICR, A Chemical Probe Targeting the Bromodomains of BAZ2A and BAZ2B. Authors: Drouin, L. / McGrath, S. / Vidler, L.R. / Chaikuad, A. / Monteiro, O. / Tallant, C. / Philpott, M. / Rogers, C. / Fedorov, O. / Liu, M. / Akhtar, W. / Hayes, A. / Raynaud, F. / Muller, S. / ...Authors: Drouin, L. / McGrath, S. / Vidler, L.R. / Chaikuad, A. / Monteiro, O. / Tallant, C. / Philpott, M. / Rogers, C. / Fedorov, O. / Liu, M. / Akhtar, W. / Hayes, A. / Raynaud, F. / Muller, S. / Knapp, S. / Hoelder, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.4 KB | Display | ![]() |
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PDB format | ![]() | 52.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 879.5 KB | Display | ![]() |
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Full document | ![]() | 880.2 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xubC ![]() 3g0lS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 13618.652 Da / Num. of mol.: 1 / Fragment: UNP residues 1858-1972 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-43C / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.44 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 36% Low Molecular Weight PEG Smears (LMW PEG smears), 0.1M MES pH 6.5 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 2, 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: 1.75→33.35 Å / Num. obs: 22857 / % possible obs: 98.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.5 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3G0L Resolution: 1.75→29.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.482 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / 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: 37.197 Å2
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Refine analyze | Luzzati coordinate error obs: 0.226 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.75→29.8 Å
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Refine LS restraints |
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