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- PDB-8uk5: Crystal structure of the bromodomain of human ATAD2B in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8uk5 | |||||||||
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Title | Crystal structure of the bromodomain of human ATAD2B in complex with histone H4S1(ph)K5ac | |||||||||
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![]() | PEPTIDE BINDING PROTEIN / bromodomain / epigenetics / chromatin reader domain / PROTEIN BINDING / histone acetylation | |||||||||
Function / homology | ![]() lysine-acetylated histone binding / histone binding / chromatin binding / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Montgomery, C. / Phillips, M. / Nix, J.C. / Glass, K.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Impact of Combinatorial Histone Modifications on Acetyllysine Recognition by the ATAD2 and ATAD2B Bromodomains. Authors: Phillips, M. / Malone, K.L. / Boyle, B.W. / Montgomery, C. / Kressy, I.A. / Joseph, F.M. / Bright, K.M. / Boyson, S.P. / Chang, S. / Nix, J.C. / Young, N.L. / Jeffers, V. / Frietze, S. / Glass, K.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 56.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.4 KB | Display | ![]() |
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Full document | ![]() | 424.5 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sdoC ![]() 8sdqC ![]() 8sdxC ![]() 8uhlC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 15826.093 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 953-1085) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q9ULI0 |
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#2: Protein/peptide | Mass: 1340.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS (pH 5.5), 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jul 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→31.37 Å / Num. obs: 33447 / % possible obs: 99.51 % / Redundancy: 11.9 % / Biso Wilson estimate: 18.27 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 28.93 |
Reflection shell | Resolution: 1.4→1.45 Å / Num. unique obs: 37316 / CC1/2: 0.873 / CC star: 0.965 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.77 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→31.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→31.37 Å
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