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- PDB-3ey3: A Conformational Transition in the Structure of a 2'-Thiomethyl-M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ey3 | ||||||||||||||||||
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Title | A Conformational Transition in the Structure of a 2'-Thiomethyl-Modified DNA Visualized at High Resolution | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Modified DNA duplex / 2'-thiomethyl uridine / modified sugar | Function / homology | STRONTIUM ION / DNA / DNA (> 10) | ![]() Method | ![]() ![]() ![]() ![]() Egli, M. / Pallan, P.S. | ![]() ![]() Title: A conformational transition in the structure of a 2'-thiomethyl-modified DNA visualized at high resolution. Authors: Pallan, P.S. / Prakash, T.P. / Li, F. / Eoff, R.L. / Manoharan, M. / 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 | ![]() | 83.1 KB | Display | ![]() |
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PDB format | ![]() | 61.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.4 KB | Display | ![]() |
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Full document | ![]() | 431.3 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ey1SC ![]() 3ey2C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3727.522 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: Chemically synthesized modified DNA (Oligonucleotide) #2: Chemical | ChemComp-SR / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.25 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 5% MPD, 20 mM Na Cacodylate pH 7.0, 6 mM Spermine tetra-HCl, 20 mM LiCl, 40 mM SrCl2., VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→6.9 Å / Num. all: 44892 / Num. obs: 43276 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.25→1.33 Å / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.92 / Num. unique all: 3321 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Modified DNA duplex alone from PDB 3EY1 (generated by using the rotation matrix -1.0 0.0 0.0; 0.0 1.0 0.0; 0.0 0.0 -1.0) Resolution: 1.25→6.9 Å / Cross valid method: THROUGHOUT / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.25→6.9 Å
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Refine LS restraints |
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