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Yorodumi- PDB-5f36: Crystal structure of the bromodomain of human ATAD2 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f36 | ||||||
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Title | Crystal structure of the bromodomain of human ATAD2 in complex with Compound A12 | ||||||
Components | ATPase family AAA domain-containing protein 2 | ||||||
Keywords | TRANSFERASE / HYDROLASE 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 / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Dong, J. / Caflisch, A. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2020 Title: Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers. Authors: Dolbois, A. / Batiste, L. / Wiedmer, L. / Dong, J. / Brutsch, M. / Huang, D. / Deerain, N.M. / Spiliotopoulos, D. / Cheng-Sanchez, I. / Laul, E. / Nevado, C. / Sledz, P. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f36.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f36.ent.gz | 55.2 KB | Display | PDB format |
PDBx/mmJSON format | 5f36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/5f36 ftp://data.pdbj.org/pub/pdb/validation_reports/f3/5f36 | HTTPS FTP |
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-Related structure data
Related structure data | 6epjC 6eptC 6epuC 6epvC 6epxC 6hi3C 6hi4C 6hi5C 6hi6C 6hi7C 6hi8C 6hiaC 6hibC 6hicC 6hidC 6hieC 3daiS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: UNP residues 981-1108 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATAD2, L16, PRO2000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PL18, EC: 3.6.1.3 |
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#2: Chemical | ChemComp-5UE / [( |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-CL / |
#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: 4.08 Å3/Da / Density % sol: 69.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 27, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→69.112 Å / Num. all: 42035 / Num. obs: 42035 / % possible obs: 99.7 % / Redundancy: 18.9 % / Biso Wilson estimate: 22.95 Å2 / Rpim(I) all: 0.01 / Rrim(I) all: 0.045 / Rsym value: 0.043 / Net I/av σ(I): 7.866 / Net I/σ(I): 35 / Num. measured all: 793117 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DAI Resolution: 1.5→48.691 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.89 / Stereochemistry target values: ML
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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 max: 97.21 Å2 / Biso mean: 35.3911 Å2 / Biso min: 16.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→48.691 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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