+Open data
-Basic information
Entry | Database: PDB / ID: 4hli | ||||||||||||||||||||
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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 | Homo sapiens (human) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hli.cif.gz | 24.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hli.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hli.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/4hli ftp://data.pdbj.org/pub/pdb/validation_reports/hl/4hli | HTTPS FTP |
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-Related structure data
Related structure data | 4gjuC 4glcC 4glgC 4glhC 1dpnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-K / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.04m sodium cacodylate buffer, 0.08M NaCCl, 0.12m KCl, 0.02m MgCl2, 0.012m spermine tetra hydrochloride, 35% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00067 / Wavelength: 1.00067 Å | |||||||||
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 |
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Reflection | Resolution: 1.99→50 Å / Num. all: 4775 / Num. obs: 4315 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.55 % / Rmerge(I) obs: 0.038 / Rsym value: 0.022 / Net I/σ(I): 21.23 | |||||||||
Reflection shell | Resolution: 1.99→2.11 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 5.81 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DPN Resolution: 1.99→50 Å / Num. parameters: 2099 / Num. restraintsaints: 2456 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 515.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→50 Å
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Refine LS restraints |
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