+Open data
-Basic information
Entry | Database: PDB / ID: 5b79 | ||||||
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Title | Crystal structure of DPF2 double PHD finger | ||||||
Components | Zinc finger protein ubi-d4 | ||||||
Keywords | METAL BINDING PROTEIN / DPF2 | ||||||
Function / homology | Function and homology information negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / regulation of G1/S transition of mitotic cell cycle ...negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / regulation of G1/S transition of mitotic cell cycle / apoptotic signaling pathway / lysine-acetylated histone binding / transcription corepressor activity / nervous system development / chromatin remodeling / intracellular membrane-bounded organelle / centrosome / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.601 Å | ||||||
Authors | Li, H. / Xiong, X. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2016 Title: Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2 Authors: Xiong, X. / Panchenko, T. / Yang, S. / Zhao, S. / Yan, P. / Zhang, W. / Xie, W. / Li, Y. / Zhao, Y. / Allis, C.D. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b79.cif.gz | 37.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b79.ent.gz | 23.9 KB | Display | PDB format |
PDBx/mmJSON format | 5b79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b79 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b79 | HTTPS FTP |
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-Related structure data
Related structure data | 5b75C 5b76C 5b77C 5b78C 4llbS 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
#1: Protein | Mass: 13818.602 Da / Num. of mol.: 1 / Fragment: UNP residues 270-391 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92785 | ||
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#2: Chemical | ChemComp-ZN / #3: 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: 2.72 Å3/Da / Density % sol: 54.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: ammonium citrate tribasic, Bis-Tris propane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→23.6 Å / Num. obs: 4902 / % possible obs: 99.6 % / Redundancy: 7.5 % / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.6→2.64 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LLB Resolution: 2.601→23.599 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.601→23.599 Å
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Refine LS restraints |
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LS refinement shell |
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