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Yorodumi- PDB-4qsv: Structure of the bromodomain of human ATPase family AAA domain-co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qsv | ||||||
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Title | Structure of the bromodomain of human ATPase family AAA domain-containing protein 2 (ATAD2) in complex with thymidine | ||||||
Components | ATPase family AAA domain-containing protein 2 | ||||||
Keywords | SIGNALING PROTEIN / Structural Genomics Consortium (SGC) / bromodomain / actyl-lysine binding / ATPase family AAA domain-containing protein 2 / epigenetics | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Chaikuad, A. / Felletar, I. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: MedChemComm / Year: 2014 Title: Structure-based approaches towards identification of fragments for the low-druggability ATAD2 bromodomain Authors: Chaikuad, A. / Petros, A.M. / Fedorov, O. / Xu, J. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qsv.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qsv.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qsv_validation.pdf.gz | 469.6 KB | Display | wwPDB validaton report |
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Full document | 4qsv_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 4qsv_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 4qsv_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/4qsv ftp://data.pdbj.org/pub/pdb/validation_reports/qs/4qsv | HTTPS FTP |
-Related structure data
Related structure data | 4qspC 4qsqC 4qsrC 4qssC 4qstC 4qsuC 4qswC 4qsxC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15453.514 Da / Num. of mol.: 1 / Fragment: bromodomain (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-R3-pRARE2 / References: UniProt: Q6PL18, EC: 3.6.1.3 | ||||
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#2: Chemical | ChemComp-SO4 / | ||||
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-THM / | #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: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, ...Details: apo crystals grew in 1.8-2.2 M ammonium sulphate, 0.1 M Bis-Tris, pH 5.5-6.5. Soaking performed in 28-32% PEG 3350, 50 mM bis-tris pH 5.5, 50 mM ammonium phosphate and 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 10, 2013 |
Radiation | Monochromator: Flat graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.27 Å / Num. all: 21004 / Num. obs: 20984 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2937 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb id: 3DAI Resolution: 1.9→30.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.546 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.104 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 36.922 Å2
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Refine analyze | Luzzati coordinate error obs: 0.225 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→30.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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