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Open data
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Basic information
Entry | Database: PDB / ID: 432d | ||||||||||||||||||
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Title | D(GGCCAATTGG) COMPLEXED WITH DAPI | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / DEOXYRIBONUCLEIC ACID / DNA-DRUG COMPLEX / TRIPLET FORMATION / 4' / 6-DIAMIDINO-2-PHENYL INDOLE / DAPI / MINOR GROOVE BINDER | Function / homology | 6-AMIDINE-2-(4-AMIDINO-PHENYL)INDOLE / DNA | ![]() Method | ![]() ![]() ![]() Vlieghe, D. / Van Meervelt, L. | ![]() ![]() Title: Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode. Authors: Vlieghe, D. / 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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Download
PDBx/mmCIF format | ![]() | 23 KB | Display | ![]() |
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PDB format | ![]() | 14.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 592.4 KB | Display | ![]() |
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Full document | ![]() | 598.9 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 6.2 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 #2: Chemical | ChemComp-DAP / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.26 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.9 Details: pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 289.0K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.89→10 Å / Num. all: 4106 / Num. obs: 4106 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.78 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 4 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 5.55 / % possible all: 95.1 |
Reflection | *PLUS Num. obs: 4115 / Num. measured all: 24368 |
Reflection shell | *PLUS % possible obs: 95.1 % |
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Processing
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Refinement | Starting model: BD0006 USED AS STARTING MODEL FOR REFINEMENT Resolution: 1.89→10 Å / Num. parameters: 2051 / Num. restraintsaints: 2080 / Cross valid method: NONE StereochEM target val spec case: DAPI DICTIONARY BASED ON CSD Stereochemistry target values: TAYLOR AND KENNARD
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 512 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→10 Å
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Refine LS restraints |
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