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- PDB-1k2z: The Crystal Structure of d(GGCCAATTGG) Complexed with Distamycin. -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k2z | ||||||||||||||||||
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Title | The Crystal Structure of d(GGCCAATTGG) Complexed with Distamycin. | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-DNA double helix / base triplets / minor groove binding / drug / distamycin | Function / homology | DISTAMYCIN A / DNA | ![]() Method | ![]() ![]() ![]() ![]() Uytterhoeven, K. / Van Meervelt, L. | ![]() ![]() Title: Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG). Authors: Uytterhoeven, K. / Sponer, J. / Van Meervelt, L. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 23.1 KB | Display | ![]() |
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PDB format | ![]() | 14.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 574 KB | Display | ![]() |
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Full document | ![]() | 582.2 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jtlC C: citing same article ( |
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Similar structure data | |
Other databases |
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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: This sequence is synthesized by Oswell DNA Service (Southampton, UK). #2: Chemical | ChemComp-DMY / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.31 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, magnesium chloride, cacodylate, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||
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: Apr 9, 1999 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9116 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. all: 2538 / Num. obs: 2351 / % possible obs: 92.7 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 5 / Redundancy: 5.5 % / Biso Wilson estimate: 80.64 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 2.38→2.42 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 113 / Rsym value: 0.251 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: NDB entry DD0002 Resolution: 2.38→100 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: user defined
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Displacement parameters | Biso mean: 72.9 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.38→100 Å
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Refine LS restraints |
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