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Yorodumi- PDB-4tt6: Crystal structure of ATAD2A bromodomain double mutant N1063A-Y106... -
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-Basic information
Entry | Database: PDB / ID: 4tt6 | ||||||
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Title | Crystal structure of ATAD2A bromodomain double mutant N1063A-Y1064A in apo form | ||||||
Components | ATPase family AAA domain-containing protein 2 | ||||||
Keywords | GENE REGULATION / acetyllysine reader deficient bromodomain | ||||||
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: 2 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 | 4tt6.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tt6.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 4tt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/4tt6 ftp://data.pdbj.org/pub/pdb/validation_reports/tt/4tt6 | HTTPS FTP |
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-Related structure data
Related structure data | 4tt2C 4tt4C 4tteC 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
#1: Protein | Mass: 15318.393 Da / Num. of mol.: 1 / Fragment: bromodomain (UNP residues 981-1108) / Mutation: N1063A and Y1064A 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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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 4.13 Å3/Da / Density % sol: 70.23 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.0M Ammonium sulfate, 0.1M Bis-Tris pH5.5 |
-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: Aug 9, 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→48.83 Å / Num. obs: 18358 / % possible obs: 100 % / Redundancy: 40.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.018 / Net I/σ(I): 31.4 / Num. measured all: 746601 / Scaling rejects: 42 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 40.2 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 8.3 / Num. measured all: 52818 / Num. unique all: 1315 / CC1/2: 0.978 / Rpim(I) all: 0.112 / Rejects: 0 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DAI Resolution: 2→48.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.23 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 230.23 Å2 / Biso mean: 24.88 Å2 / Biso min: 11.06 Å2
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Refinement step | Cycle: final / Resolution: 2→48.83 Å
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Refine LS restraints |
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