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- PDB-7d87: Crystal Structure of zebrafish PHF14-PZP in complex with H3(1-25) -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d87 | ||||||
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Title | Crystal Structure of zebrafish PHF14-PZP in complex with H3(1-25) | ||||||
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![]() | GENE REGULATION / PHF14-PZP | ||||||
Function / homology | ![]() negative regulation of mesenchymal cell proliferation involved in lung development / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of mesenchymal cell proliferation / mesenchymal cell proliferation involved in lung development / mesenchymal cell proliferation / lung alveolus development / histone reader activity / structural constituent of chromatin / nucleosome / histone binding ...negative regulation of mesenchymal cell proliferation involved in lung development / negative regulation of platelet-derived growth factor receptor-alpha signaling pathway / negative regulation of mesenchymal cell proliferation / mesenchymal cell proliferation involved in lung development / mesenchymal cell proliferation / lung alveolus development / histone reader activity / structural constituent of chromatin / nucleosome / histone binding / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, H. / Zheng, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14. Authors: Zheng, S. / Bi, Y. / Chen, H. / Gong, B. / Jia, S. / Li, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.9 KB | Display | ![]() |
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PDB format | ![]() | 75.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438 KB | Display | ![]() |
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Full document | ![]() | 441.9 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d86SC ![]() 7d8aC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 23349.238 Da / Num. of mol.: 1 / Fragment: PHF14-PZP Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 2634.090 Da / Num. of mol.: 1 / Fragment: histone H3(1-25) / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % / Mosaicity: 0.391 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.5 Details: 0.1 M Carboxylic acids,0.1 M Buffer System 2, 37.50% % v/v MPD_P1K_P3350 (morpheus). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 20, 2017 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→50 Å / Num. obs: 15363 / % possible obs: 99.8 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.037 / Rrim(I) all: 0.13 / Χ2: 1.524 / Net I/σ(I): 7 / Num. measured all: 181303 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7D86 Resolution: 2.11→32.21 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.5 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 149.4 Å2 / Biso mean: 58.8207 Å2 / Biso min: 21.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.11→32.21 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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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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