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Yorodumi- PDB-5oww: Crystal structure of human BRD4(1) bromodomain in complex with UT22B -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oww | ||||||
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Title | Crystal structure of human BRD4(1) bromodomain in complex with UT22B | ||||||
Components | Bromodomain-containing protein 4 | ||||||
Keywords | DNA BINDING PROTEIN / BRD4 bromodomain 1(BRP4(1)) / Inhibitor | ||||||
Function / homology | Function and homology information RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Zhu, J. / Caflisch, A. | ||||||
Citation | Journal: Acs Cent.Sci. / Year: 2018 Title: Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). Authors: Batiste, L. / Unzue, A. / Dolbois, A. / Hassler, F. / Wang, X. / Deerain, N. / Zhu, J. / Spiliotopoulos, D. / Nevado, C. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oww.cif.gz | 239.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5oww.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 5oww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oww_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 5oww_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5oww_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 5oww_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/5oww ftp://data.pdbj.org/pub/pdb/validation_reports/ow/5oww | HTTPS FTP |
-Related structure data
Related structure data | 5nlkC 5ovbC 5owmC 2ossS 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15099.380 Da / Num. of mol.: 4 / Fragment: Bromo domain 1, UNP residues 44-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885 #2: Chemical | ChemComp-B0Q / ~{ #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999989 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999989 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→41.92 Å / Num. obs: 85408 / % possible obs: 97.9 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.459 / Num. unique obs: 4173 / CC1/2: 0.665 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OSS Resolution: 1.5→41.094 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→41.094 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -28.3469 Å / Origin y: -6.974 Å / Origin z: 27.4421 Å
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Refinement TLS group | Selection details: all |