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Yorodumi- PDB-5ffy: Crystal structure of the bromodomain of human BRPF1 in complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ffy | ||||||
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Title | Crystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole ligand | ||||||
Components | Peregrin | ||||||
Keywords | TRANSCRIPTION / Peregrin / MOZ-MORF complex | ||||||
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 DNA-templated transcription / regulation of transcription by RNA polymerase II ...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 DNA-templated transcription / regulation of transcription by RNA polymerase II / positive 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: 1.55 Å | ||||||
Authors | Tallant, C. / Savitsky, P. / Nunez-Alonso, G. / Kopec, J. / Fedorov, O. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the bromodomain of human BRPF1 in complex with a benzimidazole ligand Authors: Tallant, C. / Savitsky, P. / Nunez-Alonso, G. / Kopec, J. / Fedorov, O. / Filippakopoulos, P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ffy.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ffy.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ffy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ffy_validation.pdf.gz | 817.1 KB | Display | wwPDB validaton report |
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Full document | 5ffy_full_validation.pdf.gz | 818.8 KB | Display | |
Data in XML | 5ffy_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 5ffy_validation.cif.gz | 11.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/5ffy ftp://data.pdbj.org/pub/pdb/validation_reports/ff/5ffy | HTTPS FTP |
-Related structure data
Related structure data | 4lc2S 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 / Fragment: UNP residues 626-740 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201 |
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#2: Chemical | ChemComp-5XD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.05 % / Description: Rod |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M bis tris propane pH 9, 10% ethylene glycol, 0.15 M sodium nitrate PH range: 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→25.19 Å / Num. all: 20656 / Num. obs: 20656 / % possible obs: 98.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.022 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.55→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.1 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LC2 Resolution: 1.55→23.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.514 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / 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: 26.718 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→23.88 Å
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