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- PDB-131d: THE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM O... -
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Open data
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Basic information
Entry | Database: PDB / ID: 131d | ||||||||||||||||||
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Title | THE LOW-TEMPERATURE CRYSTAL STRUCTURE OF THE PURE-SPERMINE FORM OF Z-DNA REVEALS BINDING OF A SPERMINE MOLECULE IN THE MINOR GROOVE | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / Z-DNA / DOUBLE HELIX | Function / homology | SPERMINE / DNA | ![]() Method | ![]() ![]() Bancroft, D. / Williams, L.D. / Rich, A. / Egli, M. | ![]() ![]() Title: The low-temperature crystal structure of the pure-spermine form of Z-DNA reveals binding of a spermine molecule in the minor groove. Authors: Bancroft, D. / Williams, L.D. / Rich, A. / Egli, M. #1: ![]() Title: Structure of the Pure-Spermine Form of Z-DNA (Magnesium Free) at 1 Angstrom Resolution Authors: Egli, M. / Williams, L.D. / Gao, Q. / Rich, 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 | ![]() | 19.1 KB | Display | ![]() |
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PDB format | ![]() | 12 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 338.9 KB | Display | ![]() |
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Full document | ![]() | 352 KB | Display | |
Data in XML | ![]() | 3.8 KB | Display | |
Data in CIF | ![]() | 4.9 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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Unit cell |
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Components
#1: DNA chain | Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.64 Å3/Da / Density % sol: 25.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7 / Details: Egli, M., (1991) Biochemistry, 30, 11388. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 163 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 1 Å / Num. all: 14081 / Num. obs: 9691 / Observed criterion σ(F): 2 |
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Processing
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Refinement | Resolution: 1→5 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1→5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1 Å / Lowest resolution: 5 Å / Num. reflection obs: 9575 / σ(F): 2 / Rfactor obs: 0.18 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |