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Open data
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Basic information
Entry | Database: PDB / ID: 4wu8 | ||||||
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Title | Structure of trPtNAP-NCP145 | ||||||
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![]() | ![]() ![]() | ||||||
Function / homology | ![]() structural constituent of chromatin / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Chua, E.Y.D. / Davey, C.A. | ||||||
![]() | ![]() Title: Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents. Authors: Chua, E.Y. / Davey, G.E. / Chin, C.F. / Droge, P. / Ang, W.H. / Davey, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325 KB | Display | ![]() |
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PDB format | ![]() | 248.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
-DNA chain , 2 types, 2 molecules IJ
#1: DNA chain | Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein , 4 types, 8 molecules AEBFCGDH
#3: Protein | Mass: 15303.930 Da / Num. of mol.: 2 / Mutation: G102A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #4: Protein | ![]() Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #5: Protein | Mass: 13978.241 Da / Num. of mol.: 2 / Mutation: G99R, A123S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #6: Protein | Mass: 13848.097 Da / Num. of mol.: 2 / Mutation: S29T Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 4 types, 41 molecules ![](data/chem/img/CX3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | #8: Chemical | ![]() #9: Chemical | ChemComp-MG / | #10: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 59.49 % |
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Crystal grow![]() | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Manganese chloride, potassium chloride, potassium cacodylate |
-Data collection
Diffraction | Mean temperature: 98.15 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.45→94.05 Å / Num. obs: 73961 / % possible obs: 93.4 % |
Reflection shell | Resolution: 2.45→2.58 Å / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 1.6 / % possible all: 68.4 |
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Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.45→94.05 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.912 / SU B: 9.092 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.386 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→94.05 Å
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