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- PDB-4tt4: Crystal structure of ATAD2A bromodomain complexed with H3(1-21)K1... -
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Basic information
Entry | Database: PDB / ID: 4tt4 | |||||||||
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Title | Crystal structure of ATAD2A bromodomain complexed with H3(1-21)K14Ac peptide | |||||||||
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![]() | GENE REGULATION / bromodomain-acetylated histone complex | |||||||||
Function / homology | ![]() nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome ...nucleosome disassembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / transcription initiation-coupled chromatin remodeling / nucleosome assembly / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Poncet-Montange, G. / Zhan, Y. / Bardenhagen, J. / Petrocchi, A. / Leo, E. / Shi, X. / Lee, G. / Leonard, P. / Geck Do, M. / Cardozo, M. ...Poncet-Montange, G. / Zhan, Y. / Bardenhagen, J. / Petrocchi, A. / Leo, E. / Shi, X. / Lee, G. / Leonard, P. / Geck Do, M. / Cardozo, M. / Palmer, W. / Andersen, J. / Jones, P. / Ladbury, J. | |||||||||
![]() | ![]() Title: Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2. Authors: Poncet-Montange, G. / Zhan, Y. / Bardenhagen, J.P. / Petrocchi, A. / Leo, E. / Shi, X. / Lee, G.R. / Leonard, P.G. / Geck Do, M.K. / Cardozo, M.G. / Andersen, J.N. / Palmer, W.S. / Jones, P. / Ladbury, J.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.1 KB | Display | ![]() |
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PDB format | ![]() | 98 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4tt2C ![]() 4tt6C ![]() 4tteC ![]() 4tu4C ![]() 4tu6C ![]() 3daiS 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: 15453.514 Da / Num. of mol.: 2 / Fragment: bromodomain (UNP residues 981-1108) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | | Mass: 490.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.14 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.0M Ammonium sulfate, 100mM Tris pH8.5. |
-Data collection
Diffraction | Mean temperature: 193 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.7→57.84 Å / Num. obs: 13680 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.084 / Net I/σ(I): 6 / Num. measured all: 91579 / Scaling rejects: 5 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DAI Resolution: 2.7→79.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 23.057 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.464 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.81 Å2 / Biso mean: 32.511 Å2 / Biso min: 17.61 Å2
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Refinement step | Cycle: final / Resolution: 2.7→79.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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