+Open data
-Basic information
Entry | Database: PDB / ID: 4glc | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | DNA dodecamer containing 5-hydroxymethyl-cytosine | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA dodecamer / epigenetics / 5-hydroxymethyl cytosine | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | Synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.831 Å | Authors | Spingler, B. / Renciuk, D. / Vorlickova, M. | Citation | Journal: Nucleic Acids Res. / Year: 2013 | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4glc.cif.gz | 23.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4glc.ent.gz | 14.8 KB | Display | PDB format |
PDBx/mmJSON format | 4glc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/4glc ftp://data.pdbj.org/pub/pdb/validation_reports/gl/4glc | HTTPS FTP |
---|
-Related structure data
Related structure data | 4gjuC 4glgC 4glhC 4hliC 1dpnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3693.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 46.04 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 7 Details: 0.04M sodium cacodylate buffer, 0.08M sodium chloride, 0.012M spermine tetra hydrochloride, 30% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00067 |
Detector | Type: DECTRIS PILATUS 2M / 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: 1.831→41.6 Å / Num. obs: 6201 / % possible obs: 97.5 % / Redundancy: 3.68 % / Rmerge(I) obs: 0.034 / Rsym value: 0.021 / Net I/σ(I): 24.06 |
Reflection shell | Resolution: 1.831→1.94 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 6.65 / % possible all: 96.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DPN Resolution: 1.831→35.2 Å / Num. parameters: 2123 / Num. restraintsaints: 2406 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 528.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.831→35.2 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
|