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Yorodumi- PDB-457d: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG): N6-METHOXY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 457d | ||||||||||||||||||
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Title | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG): N6-METHOXYADENOSINE/ THYMIDINE BASE-PAIRS IN B-DNA | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / MODIFIED NUCLEOTIDE / METHOXYADENOSINE / DNA DAMAGE / B-DNA / DOUBLE HELIX | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2 Å | Authors | Chatake, T. / Ono, A. / Ueno, Y. / Matsuda, A. / Takenaka, A. | Citation | Journal: J.Mol.Biol. / Year: 1999 | Title: Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis. Authors: Chatake, T. / Hikima, T. / Ono, A. / Ueno, Y. / Matsuda, A. / Takenaka, A. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 457d.cif.gz | 24.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb457d.ent.gz | 15.6 KB | Display | PDB format |
PDBx/mmJSON format | 457d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 457d_validation.pdf.gz | 327 KB | Display | wwPDB validaton report |
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Full document | 457d_full_validation.pdf.gz | 327.4 KB | Display | |
Data in XML | 457d_validation.xml.gz | 1.7 KB | Display | |
Data in CIF | 457d_validation.cif.gz | 2.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/57/457d ftp://data.pdbj.org/pub/pdb/validation_reports/57/457d | HTTPS FTP |
-Related 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 #2: Chemical | ChemComp-MG / | #3: 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: 2.2 Å3/Da / Density % sol: 44.18 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / Details: Chatake, T., (1999) J. Mol. Biol., 294, 1215. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 1998 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. all: 4036 / Num. obs: 4036 / % possible obs: 84.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2 % / Rmerge(I) obs: 0.199 / % possible all: 70.9 |
-Processing
Software |
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Refinement | Resolution: 2→5 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 5 Å / σ(F): 3 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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