+Open data
-Basic information
Entry | Database: PDB / ID: 1s32 | |||||||||
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Title | Molecular Recognition of the Nucleosomal 'Supergroove' | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN/DNA / Nucleosome Core Particle (NCP) / Pyrrole-Imidazole (Py-Im) hairpin polyamide / clamp / nucleosome dynamics / STRUCTURAL PROTEIN-DNA COMPLEX | |||||||||
Function / homology | Function and homology information structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Xenopus laevis (African clawed frog) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Edayathumangalam, R.S. / Weyermann, P. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s32.cif.gz | 362.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s32.ent.gz | 276.3 KB | Display | PDB format |
PDBx/mmJSON format | 1s32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s32_validation.pdf.gz | 594.1 KB | Display | wwPDB validaton report |
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Full document | 1s32_full_validation.pdf.gz | 640.8 KB | Display | |
Data in XML | 1s32_validation.xml.gz | 55.5 KB | Display | |
Data in CIF | 1s32_validation.cif.gz | 79.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/1s32 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/1s32 | HTTPS FTP |
-Related structure data
Related structure data | 1aoiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) |
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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.) Xenopus laevis (African clawed frog) / Gene: LOC121398065 / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: A0A310TTQ1, UniProt: P84233*PLUS #3: Protein | Mass: 11263.231 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398084 / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: A0A8J1LTD2, UniProt: P62799*PLUS #4: Protein | Mass: 12941.095 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h2ac14.L / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS #5: Protein | Mass: 13524.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Plasmid: pET-based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: A0A8J0U496, UniProt: P02281*PLUS |
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-Non-polymers , 9 types, 929 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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