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- PDB-5xsk: Crystal structure of PWWP-DNA complex for human hepatoma-derived ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xsk | ||||||
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Title | Crystal structure of PWWP-DNA complex for human hepatoma-derived growth factor | ||||||
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![]() | HORMONE / Growth factor | ||||||
Function / homology | ![]() cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding ...cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding / negative regulation of neuron apoptotic process / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J. / Chen, C.J. | ||||||
![]() | ![]() Title: Structure of PWWP-DNA complex at 2.84 Angstroms resolution Authors: Chen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.1 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 954.7 KB | Display | ![]() |
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Full document | ![]() | 955.8 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xslS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3013.007 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: DNA chain | Mass: 3075.026 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Protein | Mass: 13735.487 Da / Num. of mol.: 2 / Fragment: UNP residues 1-100 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 33.83 % / Description: extended dimeric shape with DNA |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Sodium nitrate, Sodium phosphate dibasic, Ammonium sulfate, Tris, Bicine, MPD, PEG 1000, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→30 Å / Num. obs: 5853 / % possible obs: 98.7 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.109 / Rsym value: 0.135 / Net I/σ(I): 17.25 |
Reflection shell | Resolution: 2.84→2.94 Å / Redundancy: 3 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 2.57 / Rsym value: 0.507 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XSL Resolution: 2.84→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.888 / SU B: 21.851 / SU ML: 0.4 / Cross valid method: THROUGHOUT / ESU R Free: 0.482 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.297 Å2
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Refinement step | Cycle: 1 / Resolution: 2.84→30 Å
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Refine LS restraints |
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