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- PDB-1edr: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG) AT 1.6 ANGSTROM -
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Open data
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Basic information
Entry | Database: PDB / ID: 1edr | ||||||||||||||||||
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Title | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGMO6AATTCGCG) AT 1.6 ANGSTROM | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID / MODIFIED NUCLEOTIDE / METHOXYADENOSINE / DAMAGED DNA | Function / homology | SPERMINE / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() Chatake, T. / Hikima, T. / Ono, A. / Ueno, Y. / Matsuda, A. / Takenaka, A. | ![]() ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.1 KB | Display | ![]() |
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PDB format | ![]() | 17.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 333.7 KB | Display | ![]() |
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Full document | ![]() | 335.3 KB | Display | |
Data in XML | ![]() | 1.8 KB | Display | |
Data in CIF | ![]() | 3.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 457dC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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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: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.26 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, MAGNESIUM ACETATE, SPERMINE TETRAHYDROCHLORIDE, NACL, SODIUM CACODYLATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | ||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.6→100 Å / Num. all: 7518 / Num. obs: 7518 / % possible obs: 79.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 14.4 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.085 / % possible all: 61.9 | |||||||||||||||
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 28875 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 59.5 % |
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Processing
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Refinement | Resolution: 1.6→5 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: PARKINSON ET AL.
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Refinement step | Cycle: LAST / Resolution: 1.6→5 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 5 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.1 |