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- PDB-473d: NI2+/GUANINE INTERACTIONS AND NETROPSIN/GUANINE STACKING IN D(CGT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 473d | ||||||||||||||||||
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Title | NI2+/GUANINE INTERACTIONS AND NETROPSIN/GUANINE STACKING IN D(CGTATATACG)2 | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / NETROPSIN/GUANINE STACKING / NI2+/GUANINE INTERACTIONS / MINOR GROOVE BINDING | Function / homology | NICKEL (II) ION / NETROPSIN / DNA | ![]() Method | ![]() ![]() ![]() Abrescia, N.G.A. / Malinina, L. / Subirana, J.A. | ![]() ![]() Title: Stacking interaction of guanine with netropsin in the minor groove of d(CGTATATACG)2. Authors: Abrescia, N.G. / Malinina, L. / Subirana, J.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 | ![]() | 25.2 KB | Display | ![]() |
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PDB format | ![]() | 15.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 604.1 KB | Display | ![]() |
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Full document | ![]() | 610.4 KB | Display | |
Data in XML | ![]() | 5 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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Unit cell |
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Components
#1: DNA chain | Mass: 3044.017 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-NT / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.02 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.2 MM DUPLEX, 10 MM NICL2, 2 MM NETROPSIN, 25 MM NA-CACODILATE (BUFFER), 4% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9058 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→20 Å / Num. all: 7613 / Num. obs: 7613 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.071 |
Reflection shell | Resolution: 1.58→1.62 Å / Rmerge(I) obs: 0.303 |
Reflection | *PLUS % possible obs: 98.6 % / Num. measured all: 40123 |
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Processing
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Refinement | Resolution: 1.58→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.58→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / Num. reflection obs: 5343 / Num. reflection Rfree: 599 / Rfactor all: 0.175 / Rfactor obs: 0.247 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |