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Yorodumi- PDB-1y7f: Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y7f | ||||||||||||||||||
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Title | Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy(methyleneamino)oxy]ethyl] Thymidine (T*) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / A-DNA / modified | Function / homology | : / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y7f.cif.gz | 24.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y7f.ent.gz | 15.2 KB | Display | PDB format |
PDBx/mmJSON format | 1y7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/1y7f ftp://data.pdbj.org/pub/pdb/validation_reports/y7/1y7f | HTTPS FTP |
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-Related structure data
Related structure data | 1wv5C 1wv6C 1y84C 1y86C 1y8lC 1y8vC 1y9fC 1y9sC 1yb9C 1ybcC 410dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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 |
-Components
#1: DNA chain | Mass: 3150.098 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-BA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.31 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 20mM Na-Cacodilate, 2mM Spermine, 5mM Barium Chloride, pH 6.3, 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 13, 1998 / 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→50 Å / Num. all: 6913 / Num. obs: 6913 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 3.4 / Num. unique all: 627 / % possible all: 90.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 410D Resolution: 1.6→17 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
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Displacement parameters | Biso mean: 23.4 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å
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