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Yorodumi- PDB-4tte: Crystal structure of ATAD2A bromodomain complexed with methyl 3-a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tte | ||||||
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Title | Crystal structure of ATAD2A bromodomain complexed with methyl 3-amino-5-(3,5-dimethyl-1,2-oxazol-4-yl)benzoate | ||||||
Components | ATPase family AAA domain-containing protein 2 | ||||||
Keywords | GENE REGULATION / ATAD2 bromodomain inhibitor complex | ||||||
Function / homology | Function and homology information Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / histone binding / chromatin binding / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | 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. | ||||||
Citation | Journal: Biochem.J. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tte.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tte.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 4tte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/4tte ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4tte | HTTPS FTP |
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-Related structure data
Related structure data | 4tt2C 4tt4C 4tt6C 4tu4C 4tu6C 3daiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 981-1108) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PL18, EC: 3.6.1.3 |
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-Non-polymers , 5 types, 257 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-36Z / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.04 Å3/Da / Density % sol: 69.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 2.1-2.4M Ammonium Sulfate, 0.1M Bis-Tris pH5.5, 10% Glycerol PH range: 5.2-5.7 |
-Data collection
Diffraction | Mean temperature: 193 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å | |||||||||||||||||||||||||||
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: 1.8→48.57 Å / Num. obs: 24459 / % possible obs: 100 % / Redundancy: 21.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.018 / Net I/σ(I): 25 / Num. measured all: 519476 / Scaling rejects: 45 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DAI Resolution: 1.8→68.68 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.925 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 86.71 Å2 / Biso mean: 30.077 Å2 / Biso min: 13.7 Å2
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Refinement step | Cycle: final / Resolution: 1.8→68.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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