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Yorodumi- PDB-5o5f: Crystal structure of the human BRPF1 bromodomain in complex with BZ038 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o5f | ||||||
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Title | Crystal structure of the human BRPF1 bromodomain in complex with BZ038 | ||||||
Components | Peregrin | ||||||
Keywords | DNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription | ||||||
Function / homology | Function and homology information acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription ...acetyltransferase activator activity / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.302 Å | ||||||
Authors | Zhu, J. / Caflisch, A. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 Title: Structure-based discovery of selective BRPF1 bromodomain inhibitors. Authors: Zhu, J. / Zhou, 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 | 5o5f.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o5f.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o5f_validation.pdf.gz | 749.8 KB | Display | wwPDB validaton report |
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Full document | 5o5f_full_validation.pdf.gz | 751.6 KB | Display | |
Data in XML | 5o5f_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 5o5f_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/5o5f ftp://data.pdbj.org/pub/pdb/validation_reports/o5/5o5f | HTTPS FTP |
-Related structure data
Related structure data | 5mwgC 5mwhC 5mwzC 5o4sC 5o4tC 5o55C 5o5aC 5o5hC 5ov8C 5owaC 6ekqC 4lc2S 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: 13703.698 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201 | ||
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#2: Chemical | ChemComp-9LT / | ||
#3: Chemical | #4: 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: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-tris propane, pH6.5, 0.2 M Sodium Nitrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→40.52 Å / Num. obs: 33637 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 1 / Rmerge(I) obs: 0.022 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1591 / CC1/2: 0.802 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Starting model: 4LC2 Resolution: 1.302→30.382 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.302→30.382 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: 27.6128 Å / Origin y: 1.7403 Å / Origin z: -9.6875 Å
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Refinement TLS group | Selection details: all |