+Open data
-Basic information
Entry | Database: PDB / ID: 5xfp | ||||||
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Title | Binary complex of PHF1 and a double stranded DNA | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / PHF1 / PCL1 / DNA / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information histone methyltransferase binding / DNA repair-dependent chromatin remodeling / methylated histone binding / transcription corepressor binding / PRC2 methylates histones and DNA / site of double-strand break / chromatin organization / 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 / site of double-strand break / chromatin organization / centrosome / chromatin binding / regulation of DNA-templated transcription / DNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wang, Z. / Li, H. | ||||||
Citation | Journal: Nature / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xfp.cif.gz | 405.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xfp.ent.gz | 327.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xfp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/5xfp ftp://data.pdbj.org/pub/pdb/validation_reports/xf/5xfp | HTTPS FTP |
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-Related structure data
Related structure data | 5xfnSC 5xfoC 5xfqC 5xfrC 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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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.) Homo sapiens (human) / Gene: PHF1, PCL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O43189 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97791 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |