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Yorodumi- PDB-5dy7: Crystal structure of the human BRPF1 bromodomain in complex with SEED4 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dy7 | ||||||
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Title | Crystal structure of the human BRPF1 bromodomain in complex with SEED4 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Zhu, J. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: Twenty Crystal Structures of Bromodomain and PHD Finger Containing Protein 1 (BRPF1)/Ligand Complexes Reveal Conserved Binding Motifs and Rare Interactions. Authors: Zhu, J. / Caflisch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dy7.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dy7.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 5dy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dy7_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 5dy7_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 5dy7_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 5dy7_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/5dy7 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/5dy7 | HTTPS FTP |
-Related structure data
Related structure data | 5c7nC 5c85C 5c87C 5dyaC 5dycC 5e3dC 5e3gC 5em3C 5eprC 5epsC 5eq1C 5etbC 5etdC 5ev9C 5evaC 5ewcC 5ewdC 5ewhC 4lc2S 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: 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-5GT / |
#3: Chemical | ChemComp-NO3 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M Sodium Acetate, pH5.5, 0.15 M Sodium Nitrate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→40.19 Å / Num. obs: 15153 / % possible obs: 99.2 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.69→1.78 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.5 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LC2 Resolution: 1.69→40.186 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.72 / 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: 1.69→40.186 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: 27.0249 Å / Origin y: 1.7388 Å / Origin z: -9.91 Å
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Refinement TLS group | Selection details: all |