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- PDB-1g8n: MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURID... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g8n | ||||||||||||||||||
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Title | MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / MODIFIED NUCLEOTIDE / FORMYLURIDINE / DNA DAMAGE / B-DNA / DOUBLE HELIX / DEOXYRIBONUCLEIC ACID | Function / homology | DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Tsunoda, M. / Karino, N. / Ueno, Y. / Matsuda, A. / Takenaka, A. | ![]() ![]() Title: Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers? Authors: Tsunoda, M. / Karino, N. / 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 | ![]() | 28.4 KB | Display | ![]() |
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PDB format | ![]() | 18.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 320.1 KB | Display | ![]() |
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Full document | ![]() | 320.1 KB | Display | |
Data in XML | ![]() | 1.4 KB | Display | |
Data in CIF | ![]() | 2.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g75C ![]() 1g8uC ![]() 1g8vC ![]() 355dS S: Starting model for refinement 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: 3677.376 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: 2.2 Å3/Da / Density % sol: 44.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, spermine, magnesium chloride, sodium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
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: Jun 10, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 88610 / Num. obs: 10301 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.6 % / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.228 / % possible all: 97.2 |
Reflection | *PLUS Num. measured all: 88610 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 355D Resolution: 1.55→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.55→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.65 Å / Rfactor Rfree error: 0.03 /
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / Rfactor obs: 0.207 / % reflection Rfree: 10 % | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.363 / Rfactor Rwork: 0.36 |