[English] 日本語
Yorodumi- PDB-1y84: Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(imidazo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y84 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(imidazolyl)ethyl] Thymidine (T*) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / A-DNA / O2'-modification / decamer. | Function / homology | SPERMINE / DNA | Function and homology information Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | 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. | Citation | Journal: Biochemistry / Year: 2005 | 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1y84.cif.gz | 26.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1y84.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 1y84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y84 ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y84 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1wv5C 1wv6C 1y7fC 1y86C 1y8lC 1y8vC 1y9fC 1y9sC 1yb9C 1ybcC 410dS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | Chains A and B form duplex |
-Components
#1: DNA chain | Mass: 3155.119 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Chemical | ChemComp-SPM / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.34 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM NaCL, 12mM KCL, 20mM MgCL2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jul 6, 1999 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. all: 6710 / Num. obs: 6710 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.9 / Num. unique all: 619 / % possible all: 95.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 410D Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: Conjugate gradient refinement using maximum likelihood target for amplitudes
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.64 Å
|