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Yorodumi- PDB-5b76: Crystal structure of MOZ double PHD finger domain in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b76 | |||||||||
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Title | Crystal structure of MOZ double PHD finger domain in complex with histone H3 crotonylation at K14 | |||||||||
Components |
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Keywords | TRANSFERASE / double PHD finger | |||||||||
Function / homology | Function and homology information histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation ...histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation / acetyltransferase activity / chromosome organization / histone acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / regulation of signal transduction by p53 class mediator / transcription coregulator activity / PML body / nucleosome assembly / structural constituent of chromatin / nucleosome / cellular senescence / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of gene expression / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 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 | 5b76.cif.gz | 103.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b76.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 5b76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b76 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b76 | HTTPS FTP |
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-Related structure data
Related structure data | 5b75C 5b77C 5b78C 5b79C 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: 14930.603 Da / Num. of mol.: 1 / Fragment: UNP residues 194-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MOZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q92794, histone acetyltransferase | ||||
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#2: Protein/peptide | Mass: 2699.164 Da / Num. of mol.: 1 / Fragment: UNP residues 2-26 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: K7EMV3 | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 2.46 Å3/Da / Density % sol: 50.07 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / Details: polyethylene glycol 4000, lithium sulfate, Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97893 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→24.1 Å / Num. obs: 21315 / % possible obs: 99.5 % / Redundancy: 8.6 % / Net I/σ(I): 44.2 |
Reflection shell | Resolution: 1.65→1.68 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LLB Resolution: 1.653→24.06 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.653→24.06 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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