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Open data
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Basic information
Entry | Database: PDB / ID: 2i2i | ||||||||||||||||||
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Title | Crystal structure of the DB293-D(CGCGAATTCGCG)2 complex. | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-TYPE DNA DODECAMER WITH COMPOUND DB 293. | Function / homology | Chem-MBC / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Lee, M.P.H. / Neidle, S. | ![]() ![]() Title: Crystal structure of the DB293-D(CGCGAATTCGCG)2 complex. Authors: Lee, M.P.H. / Neidle, S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 26.4 KB | Display | ![]() |
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PDB format | ![]() | 16.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 608.1 KB | Display | ![]() |
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Full document | ![]() | 609 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dbeS S: Starting model for refinement |
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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: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: AT-RICH REGION IN THE GENOME OF ORGANISMS. #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-MBC / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.48 % | ||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 7 Details: MAGNESIUM CHLORIDE, DNA DODECAMER, MPD, COMPOUND DB 293, SODIUM CACODYLATE BUFFER., pH 7.0, VAPOR DIFFUSION, HANGING DROP, pH 7.00 | ||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 7, 2006 / Details: OSMIC FOCUSING MIRROR SYSTEM |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→25.34 Å / Num. obs: 8262 / % possible obs: 98.6 % / Observed criterion σ(I): 3 / Redundancy: 3.36 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 3.7 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DNA PART OF NDB ENTRY GDL009 OR PDB ENTRY 2DBE. Resolution: 1.63→8 Å / Num. parameters: 2379 / Num. restraintsaints: 2537 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 594 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→8 Å
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Refine LS restraints |
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