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Open data
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Basic information
Entry | Database: PDB / ID: 5ckk | ||||||
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Title | Crystal structure of 9DB1* deoxyribozyme | ||||||
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![]() | LIGASE / deoxyribozyme / RNA-ligase / catalytic DNA | ||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10)![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ponce-Salvatierra, A. / Hoebartner, C. / Pena, V. | ||||||
![]() | ![]() Title: Crystal structure of a DNA catalyst. Authors: Ponce-Salvatierra, A. / Wawrzyniak-Turek, K. / Steuerwald, U. / Hobartner, C. / Pena, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 244.4 KB | Display | ![]() |
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Full document | ![]() | 244.3 KB | Display | |
Data in XML | ![]() | 1015 B | Display | |
Data in CIF | ![]() | 1.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ckiSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: DNA chain | Mass: 13651.733 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: RNA chain | Mass: 4831.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, spermine, magnesium chloride, sodium chloride, sodium cacodylate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→41.58 Å / Num. obs: 5146 / % possible obs: 97 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.87 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 25.8 % / Rmerge(I) obs: 6.13 / Mean I/σ(I) obs: 0.43 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CKI Resolution: 2.801→46.446 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.801→46.446 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 4.3772 Å / Origin y: -23.6843 Å / Origin z: 9.4008 Å
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Refinement TLS group | Selection details: chain 'D' or chain 'Y' |