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Open data
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Basic information
Entry | Database: PDB / ID: 4glh | ||||||||||||||||||||
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Title | DNA dodecamer containing 5-hydroxymethyl cytosine | ||||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / B-DNA dodecamer / epigenetics / 5-hydroxymethyl cytosine | Function / homology | : / DNA / DNA (> 10) | ![]() Biological species | Synthetic construct (others) | Method | ![]() ![]() ![]() ![]() Spingler, B. / Renciuk, D. / Vorlickova, M. | ![]() ![]() Title: Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine. Authors: Renciuk, D. / Blacque, O. / Vorlickova, M. / Spingler, B. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.2 KB | Display | ![]() |
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PDB format | ![]() | 26.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 385.9 KB | Display | ![]() |
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Full document | ![]() | 388.1 KB | Display | |
Data in XML | ![]() | 4.2 KB | Display | |
Data in CIF | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gjuC ![]() 4glcC ![]() 4glgC ![]() 4hliC ![]() 1dpnS 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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Unit cell |
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Components
#1: DNA chain | Mass: 3693.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.04M sodium cacodylate buffer, 0.08M potassium chloride, 0.012M sodium chloride, 0.012M spermine tetra hydrochloride, 37% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 9, 2012 |
Radiation | Monochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00067 Å / Relative weight: 1 |
Reflection | Resolution: 1.662→41.78 Å / Num. all: 8542 / Num. obs: 7781 / % possible obs: 99.4 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3.61 % / Rmerge(I) obs: 0.025 / Rsym value: 0.0152 / Net I/σ(I): 28.66 |
Reflection shell | Resolution: 1.662→1.76 Å / Redundancy: 3.71 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 6.93 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DPN Resolution: 1.662→41.78 Å / Num. parameters: 4703 / Num. restraintsaints: 10869 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 552.3 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.662→41.78 Å
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Refine LS restraints |
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