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Yorodumi- PDB-5ye4: Crystal structure of the complex of di-acetylated histone H4 and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ye4 | ||||||
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Title | Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment | ||||||
Components |
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Keywords | NUCLEAR PROTEIN / Antibody / Histone / Complex | ||||||
Function / homology | Function and homology information arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / lipoxygenase pathway / arachidonate metabolic process / lipid oxidation / hepoxilin biosynthetic process / linoleic acid metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å | ||||||
Authors | Matsuda, T. / Ito, T. / Wakamori, M. / Umehara, T. | ||||||
Citation | Journal: Epigenetics / Year: 2018 Title: JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states. Authors: Handoko, L. / Kaczkowski, B. / Hon, C.C. / Lizio, M. / Wakamori, M. / Matsuda, T. / Ito, T. / Jeyamohan, P. / Sato, Y. / Sakamoto, K. / Yokoyama, S. / Kimura, H. / Minoda, A. / Umehara, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ye4.cif.gz | 201.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ye4.ent.gz | 158.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ye4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ye4_validation.pdf.gz | 481 KB | Display | wwPDB validaton report |
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Full document | 5ye4_full_validation.pdf.gz | 489 KB | Display | |
Data in XML | 5ye4_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 5ye4_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/5ye4 ftp://data.pdbj.org/pub/pdb/validation_reports/ye/5ye4 | HTTPS FTP |
-Related structure data
Related structure data | 5ye3C 1fj1S 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 22632.248 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) #2: Antibody | Mass: 23746.260 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) #3: Protein/peptide | Mass: 1187.353 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805*PLUS #4: Chemical | ChemComp-ZN / #5: 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: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM imidazole (pH 6.5), 150 mM zinc acetate, and 17.5% (w/v) PEG3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 287775 / % possible obs: 99 % / Redundancy: 3.5 % / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rsym value: 0.334 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FJ1 Resolution: 1.799→37.761 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.21 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.799→37.761 Å
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Refine LS restraints |
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LS refinement shell |
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