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- PDB-1ybc: Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(benzylo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ybc | ||||||||||||||||||
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Title | Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(benzyloxy)ethyl] Thymidine (T*) | ||||||||||||||||||
![]() | 5'-D(*![]() ![]() ![]() ![]() Function / homology | STRONTIUM ION / | ![]() ![]() Method | ![]() ![]() ![]() Egli, M. / Minasov, G. / Tereshko, V. / Pallan, P.S. / Teplova, M. / Inamati, G.B. / Lesnik, E.A. / Owens, S.R. / Ross, B.S. / Prakash, T.P. / Manoharan, M. | ![]() ![]() Title: Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of ...Title: Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. Authors: Egli, M. / Minasov, G. / Tereshko, V. / Pallan, P.S. / Teplova, M. / Inamati, G.B. / Lesnik, E.A. / Owens, S.R. / Ross, B.S. / Prakash, T.P. / Manoharan, 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 | ![]() | 25 KB | Display | ![]() |
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PDB format | ![]() | 15.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1wv5C ![]() 1wv6C ![]() 1y7fC ![]() 1y84C ![]() 1y86C ![]() 1y8lC ![]() 1y8vC ![]() 1y9fC ![]() 1y9sC ![]() 1yb9C ![]() 410dS C: citing same article ( 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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1 |
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Unit cell |
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Details | Chains A and B form duplex |
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Components
#1: DNA chain | Mass: 3195.180 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-SR / | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.8 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM SrCL2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 30, 1998 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→25 Å / Num. all: 5065 / Num. obs: 5065 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.348 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.2 / Num. unique all: 450 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 410D Resolution: 1.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 Details: Conjugate gradient refinement using maximum likelihood target for amplitudes
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Displacement parameters | Biso mean: 25.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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