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Open data
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Basic information
Entry | Database: PDB / ID: 1s32 | |||||||||
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Title | Molecular Recognition of the Nucleosomal 'Supergroove' | |||||||||
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![]() | STRUCTURAL PROTEIN/DNA / Nucleosome Core Particle (NCP) / Pyrrole-Imidazole (Py-Im) hairpin polyamide / clamp / nucleosome dynamics / STRUCTURAL PROTEIN-DNA COMPLEX | |||||||||
Function / homology | ![]() structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Edayathumangalam, R.S. / Weyermann, P. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K. | |||||||||
![]() | ![]() Title: Molecular Recognition of the Nucleosomal 'Supergroove' Authors: Edayathumangalam, R.S. / Weyermann, P. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 362.9 KB | Display | ![]() |
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PDB format | ![]() | 276.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1aoiS 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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Unit cell |
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Components
-DNA chain , 1 types, 2 molecules IJ
#1: DNA chain | Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Protein , 4 types, 8 molecules AEBFCGDH
#2: Protein | Mass: 15303.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 12941.095 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 929 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/IMT.gif)
![](data/chem/img/PYB.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/BAL.gif)
![](data/chem/img/DIB.gif)
![](data/chem/img/OGG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/IMT.gif)
![](data/chem/img/PYB.gif)
![](data/chem/img/ABU.gif)
![](data/chem/img/BAL.gif)
![](data/chem/img/DIB.gif)
![](data/chem/img/OGG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-IMT / #8: Chemical | ChemComp-PYB / #9: Chemical | #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-OGG / | #13: Chemical | ChemComp-CL / #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.56 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→100 Å / Num. obs: 124523 / % possible obs: 94.4 % / Redundancy: 4.75 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 22.99 |
Reflection shell | Resolution: 2.05→2.1 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.04 / % possible all: 54.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AOI Resolution: 2.05→100 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: THE STRUCTURE HAS SOME UNMODELLED POTENTIAL ALTERNATE AMINO ACID SIDE CHAIN CONFORMERS, SOLVENT ENTITIES AND SOME UNACCOUNTED SPURIOUS DENSITY.
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Refinement step | Cycle: LAST / Resolution: 2.05→100 Å
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Refine LS restraints |
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