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Yorodumi- PDB-5d7x: Crystal structure of the human BRPF1 bromodomain in complex with XZ08 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d7x | ||||||
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Title | Crystal structure of the human BRPF1 bromodomain in complex with XZ08 | ||||||
Components | Peregrin | ||||||
Keywords | DNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor | ||||||
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: 1.35 Å | ||||||
Authors | Zhu, J. / Caflisch, A. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 Title: The "Gatekeeper" Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains. Authors: Unzue, A. / Zhao, H. / Lolli, G. / Dong, J. / Zhu, J. / Zechner, M. / Dolbois, A. / Caflisch, A. / Nevado, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d7x.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d7x.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 5d7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d7x_validation.pdf.gz | 831.6 KB | Display | wwPDB validaton report |
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Full document | 5d7x_full_validation.pdf.gz | 833.9 KB | Display | |
Data in XML | 5d7x_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5d7x_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/5d7x ftp://data.pdbj.org/pub/pdb/validation_reports/d7/5d7x | HTTPS FTP |
-Related structure data
Related structure data | 5e73C 5e74C 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 / Fragment: UNP residues 626-740 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-NO3 / |
#3: Chemical | ChemComp-XZ8 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M Bis-Tris Propane, pH6.5, 0.2M 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: 1.35→40.39 Å / Num. obs: 29544 / % possible obs: 98.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 5.7 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LC2 Resolution: 1.35→30.183 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 16.9 / 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: 1.35→30.183 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: 14.6668 Å / Origin y: -23.4075 Å / Origin z: 0.5686 Å
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Refinement TLS group | Selection details: all |