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Yorodumi- PDB-223d: DIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A CYTOSINE-THYMIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 223d | ||||||||||||||||||
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Title | DIRECT OBSERVATION OF TWO BASE-PAIRING MODES OF A CYTOSINE-THYMINE ANALOGUE WITH GUANINE IN A DNA Z-FORM DUPLEX: SIGNIFICANCE FOR BASE ANALOGUE MUTAGENESIS | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / Z-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | Authors | Moore, M.H. / Van Meervelt, L. / Salisbury, S.A. / Kong Thoo Lin, P. / Brown, D.M. | Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Direct observation of two base-pairing modes of a cytosine-thymine analogue with guanine in a DNA Z-form duplex: significance for base analogue mutagenesis. Authors: Moore, M.H. / Van Meervelt, L. / Salisbury, S.A. / Lin, P.K. / Brown, D.M. #1: Journal: Nucleosides and Nucleotides / Year: 1995 Title: To Wobble or Not to Wobble: Modified Bases Incorporated Into DNA Authors: Van Meervelt, L. / Moore, M.H. / Kong Thoo Lin, P. / Brown, D.M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 223d.cif.gz | 18.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb223d.ent.gz | 11 KB | Display | PDB format |
PDBx/mmJSON format | 223d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 223d_validation.pdf.gz | 372.5 KB | Display | wwPDB validaton report |
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Full document | 223d_full_validation.pdf.gz | 392.7 KB | Display | |
Data in XML | 223d_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 223d_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/23/223d ftp://data.pdbj.org/pub/pdb/validation_reports/23/223d | 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: 1852.242 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 25.44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, temperature 277.00K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Rmerge(I) obs: 0.004 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ZDF002 Resolution: 1.7→8 Å / σ(F): 4 /
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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Software | *PLUS Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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