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Open data
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Basic information
Entry | Database: PDB / ID: 1z8v | ||||||||||||||||||
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Title | The Structure of d(GGCCAATTGG) Complexed with Netropsin | ||||||||||||||||||
![]() | (5'-D(*![]() DNA / B-DNA DOUBLE HELIX / BASE TRIPLETS / MINOR GROOVE BINDER / DRUG / NETROPSIN | Function / homology | NETROPSIN / DNA | ![]() Method | ![]() ![]() ![]() ![]() Van Hecke, K. / Nam, P.C. / Nguyen, M.T. / Van Meervelt, L. | ![]() ![]() Title: Netropsin interactions in the minor groove of d(GGCCAATTGG) studied by a combination of resolution enhancement and ab initio calculations. Authors: Van Hecke, K. / Nam, P.C. / Nguyen, M.T. / Van Meervelt, L. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 23.5 KB | Display | ![]() |
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PDB format | ![]() | 15.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 600.2 KB | Display | ![]() |
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Full document | ![]() | 608.5 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 6.6 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: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The oligonucleotide was purchased from Oswel DNA service (University of Southampton, UK) #2: Chemical | ChemComp-NT / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.14 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6 Details: potassium cacodylate, MPD, magnesium chloride, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8457 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 5724 / % possible obs: 98.1 % / Redundancy: 10.7 % / Biso Wilson estimate: 24.74 Å2 / Rsym value: 0.04 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.75→1.81 Å / Num. unique all: 538 / Rsym value: 0.199 / % possible all: 96.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NDB ENTRY DD0002 Resolution: 1.75→9.6 Å / Isotropic thermal model: isotropic /
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Displacement parameters | Biso mean: 35.7 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→9.6 Å
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