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- PDB-2p8d: The Structure of the Dickerson Sequence with an Incorporated CeNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p8d | ||||||||||||||||||
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Title | The Structure of the Dickerson Sequence with an Incorporated CeNA Residue | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / CeNA / sugar modification | Function / homology | COBALT HEXAMMINE(III) / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Robeyns, K. / Van Meervelt, L. | ![]() ![]() Title: Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG). Authors: Robeyns, K. / Herdewijn, P. / 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 | ![]() | 25.9 KB | Display | ![]() |
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PDB format | ![]() | 17.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 403.7 KB | Display | ![]() |
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Full document | ![]() | 404.3 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 355dS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly of chain A is generated by the two fold axis: -x-1, y, -z-0.5 / The second part of the biological assembly of chain B is generated by the two fold axis: x, -y, -z |
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Components
#1: DNA chain | Mass: 3673.430 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The XAR (Cyclohexene nucleic acid) residues as well as the oligomer sequence were synthesized. #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.91 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20mM potassium cacodylate buffer (pH=5.5), 10mM cobalt hexamine, 44mM potassium chloride, 6mM sodium chloride, 5%(v/v) 2-methyl-2,4-pentanediol (MPD), and 0.75mM ssDNA against a 35%(v/v) MPD ...Details: 20mM potassium cacodylate buffer (pH=5.5), 10mM cobalt hexamine, 44mM potassium chloride, 6mM sodium chloride, 5%(v/v) 2-methyl-2,4-pentanediol (MPD), and 0.75mM ssDNA against a 35%(v/v) MPD stock solution, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8414 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 5476 / Num. obs: 5476 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3 / Num. unique all: 777 / Rsym value: 0.457 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 355D Resolution: 1.9→17.76 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.408 / SU ML: 0.148 / Isotropic thermal model: Idotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.194 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.161 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→17.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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