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- PDB-1d53: CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1d53 | ||||||
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Title | CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN OCTANUCLEOTIDE CONTAINING INOSINE, AND ITS COMPARISON WITH D(CGCG) AND D(CGCGCG) STRUCTURES | ||||||
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![]() | DNA / Z-DNA / DOUBLE HELIX | ||||||
Function / homology | DNA![]() | ||||||
Method | ![]() | ||||||
![]() | Kumar, V.D. / Harrison, R.W. / Andrews, L.C. / Weber, I.T. | ||||||
![]() | ![]() Title: Crystal structure at 1.5-A resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures. Authors: Kumar, V.D. / Harrison, R.W. / Andrews, L.C. / Weber, I.T. #1: ![]() Title: The Molecular Structure of the Left-Handed Z-DNA Double Helix at 1.0 Angstrom Atomic Resolution. Geometry, Conformation, and Ionic Interaction of d(CGCGCG) Authors: Gessner, R.V. / Frederick, C.A. / Quigley, G.J. / Rich, A. / Wang, A.H.-J. #2: ![]() Title: The Octamers d(CGCGCGCG) and d(CGCATGCG) Both Crystallize as Z-DNA in the Same Hexagonal Lattice Authors: Fujii, S. / Wang, A.H.-J. / Quigley, G.J. / Westerink, H. / Van Der Marel, G. / Van Boom, J.H. / Rich, A. #3: ![]() Title: The Tetramer d(CpGpCpG) Crystallizes as a Left-Handed Double Helix Authors: Crawford, J.L. / Kolpak, F.J. / Wang, A.H.-J. / Quigley, G.J. / Van Boom, J.H. / Van Der Marel, G. / Rich, A. #4: ![]() Title: High-Salt d(CpGpCpG), a Left-Handed Z'DNA Double Helix Authors: Drew, H. / Takano, T. / Tanaka, S. / Itakura, K. / Dickerson, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 18.9 KB | Display | ![]() |
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PDB format | ![]() | 11.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 320.3 KB | Display | ![]() |
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Full document | ![]() | 345.1 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 573.430 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28.36 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP / Temp details: ROOM TEMPERATURE | |||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.5→10 Å / Num. all: 9882 / Num. obs: 1971 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. all: 2134 / Num. measured all: 9882 / Rmerge(I) obs: 0.081 |
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Processing
Software |
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Refinement | Resolution: 1.5→5 Å / σ(F): 3 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.5→5 Å
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 5 Å / σ(F): 3 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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