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- PDB-1j8l: Molecular and Crystal Structure of D(CGCAAATTMO4CGCG): the Watson... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j8l | ||||||||||||||||||
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Title | Molecular and Crystal Structure of D(CGCAAATTMO4CGCG): the Watson-Crick Type N4-Methoxycytidine/Adenosine Base Pair in B-DNA | ||||||||||||||||||
![]() | DNA (5'-D(*![]() DNA / N4-METHOXYCYTOSINE / DNA DAMAGE / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Hossain, M.T. / Sunami, T. / Tsunoda, M. / Hikima, T. / Chatake, T. / Ueno, Y. / Matsuda, A. / Takenaka, A. | ![]() ![]() Title: Crystallographic studies on damaged DNAs IV. N(4)-methoxycytosine shows a second face for Watson-Crick base-pairing, leading to purine transition mutagenesis. Authors: Hossain, M.T. / Sunami, T. / Tsunoda, M. / Hikima, T. / Chatake, T. / 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 | ![]() | 25.8 KB | Display | ![]() |
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PDB format | ![]() | 16.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 373 KB | Display | ![]() |
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Full document | ![]() | 373.1 KB | Display | |
Data in XML | ![]() | 4.3 KB | Display | |
Data in CIF | ![]() | 5.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 355dS S: Starting model for refinement |
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Similar structure data |
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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: 3677.419 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, spermine, magnesium acetate, sodium cacodylate, sodum chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 12, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. all: 62759 / Num. obs: 7855 / % possible obs: 86.1 % / Redundancy: 8 % / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.132 / Mean I/σ(I) obs: 5.5 / % possible all: 38.4 |
Reflection | *PLUS Lowest resolution: 100 Å / Redundancy: 5.1 % / Num. measured all: 62759 |
Reflection shell | *PLUS % possible obs: 38.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 355D Resolution: 1.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å / Rfactor Rfree error: 0.124
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 % / Rfactor obs: 0.218 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.6 Å / Rfactor Rfree: 0.277 / Num. reflection Rfree: 5.2 / Rfactor Rwork: 0.206 |