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Yorodumi- PDB-4qkk: Crystal structure of an oligonucleotide containing 5-formylcytosine -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qkk | ||||||||||||||||||||
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Title | Crystal structure of an oligonucleotide containing 5-formylcytosine | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Oligonucleotide / Epigenetic Ten-Eleven / Translocation proteins / Thymine DNA glycosylase / Formylcytosine | Function / homology | DNA / DNA (> 10) | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / P-SAD / Resolution: 1.4 Å | Authors | Raiber, E.-A. / Murat, P. / Chirgadze, D.Y. / Luisi, B.F. / Balasubramanian, S. | Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 | Title: 5-Formylcytosine alters the structure of the DNA double helix. Authors: Raiber, E.A. / Murat, P. / Chirgadze, D.Y. / Beraldi, D. / Luisi, B.F. / Balasubramanian, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qkk.cif.gz | 27.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qkk.ent.gz | 19.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qkk_validation.pdf.gz | 366.4 KB | Display | wwPDB validaton report |
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Full document | 4qkk_full_validation.pdf.gz | 368.5 KB | Display | |
Data in XML | 4qkk_validation.xml.gz | 3.3 KB | Display | |
Data in CIF | 4qkk_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/4qkk ftp://data.pdbj.org/pub/pdb/validation_reports/qk/4qkk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3747.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.01M magnesium sulphate, 0.05M sodium cacodylate, 1.8M lithium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→46.25 Å / Num. all: 9608 / Num. obs: 9608 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.1715 / Mean I/σ(I) obs: 2 / Num. unique all: 1347 / Rsym value: 0.1715 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: P-SAD / Resolution: 1.4→25.974 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.42 / 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: 1.4→25.974 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %
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