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Open data
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Basic information
Entry | Database: PDB / ID: 5xfp | ||||||
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Title | Binary complex of PHF1 and a double stranded DNA | ||||||
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![]() | TRANSCRIPTION/DNA / PHF1 / PCL1 / DNA / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() histone methyltransferase binding / DNA repair-dependent chromatin remodeling / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / chromatin organization / site of double-strand break / centrosome / chromatin binding / regulation of DNA-templated transcription ...histone methyltransferase binding / DNA repair-dependent chromatin remodeling / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / chromatin organization / site of double-strand break / centrosome / chromatin binding / regulation of DNA-templated transcription / DNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Z. / Li, H. | ||||||
![]() | ![]() Title: Polycomb-like proteins link the PRC2 complex to CpG islands Authors: Li, H. / Liefke, R. / Jiang, J. / Kurland, J.V. / Tian, W. / Deng, P. / Zhang, W. / He, Q. / Patel, D.J. / Bulyk, M.L. / Shi, Y. / Wang, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 405.7 KB | Display | ![]() |
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PDB format | ![]() | 327.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.3 KB | Display | ![]() |
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Full document | ![]() | 478.9 KB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 48.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xfnSC ![]() 5xfoC ![]() 5xfqC ![]() 5xfrC 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 37700.469 Da / Num. of mol.: 3 / Fragment: UNP residues 25-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 3969.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1M Tris-pH 8.5, 25% PEG 3350, 0.2M Li2SO4, 10mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97791 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 65188 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / Num. unique all: 3189 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XFN Resolution: 2.3→49.765 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.765 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: 135.501 Å / Origin y: 24.674 Å / Origin z: 19.517 Å
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Refinement TLS group | Selection details: all |