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- PDB-1ma8: A-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridine -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ma8 | ||||||||||||||||||
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Title | A-DNA decamer GCGTA(UMS)ACGC with incorporated 2'-methylseleno-uridine | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / 2'-methylseleno-uridine | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() ![]() Teplova, M. / Wilds, C.J. / Wawrzak, Z. / Tereshko, V. / Du, Q. / Carrasco, N. / Huang, Z. / Egli, M. | ![]() ![]() Title: Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle Authors: Teplova, M. / Wilds, C.J. / Wawrzak, Z. / Tereshko, V. / Du, Q. / Carrasco, N. / Huang, Z. / Egli, M. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.6 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 326.6 KB | Display | ![]() |
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Full document | ![]() | 334.4 KB | Display | |
Data in XML | ![]() | 2.8 KB | Display | |
Data in CIF | ![]() | 4.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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: 3123.965 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: U-Se-modified DNA duplex #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.63 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MPD, spermine tetrahydrochloride, potassium chloride, sodium chloride, sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: May 30, 2001 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. obs: 23332 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rsym value: 0.049 |
Reflection shell | Resolution: 1.3→1.35 Å / Rsym value: 0.263 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.263 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection all: 23279 / % reflection Rfree: 5 % / Rfactor obs: 0.154 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |