+Open data
-Basic information
Entry | Database: PDB / ID: 8his | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of DNA decamer containing GuNA[Me,tBu] | |||||||||||||||||||||||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / OLIGONUCLEOTIDE / MODIFIED BASE | Function / homology | CACODYLIC ACID / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å | Authors | Aoyama, H. / Obika, S. / Yamaguchi, T. | Funding support | Japan, 8items |
Citation | Journal: Nucleic Acids Res. / Year: 2023 | Title: Mechanism of the extremely high duplex-forming ability of oligonucleotides modified with N-tert-butylguanidine- or N-tert-butyl-N'- methylguanidine-bridged nucleic acids. Authors: Yamaguchi, T. / Horie, N. / Aoyama, H. / Kumagai, S. / Obika, S. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8his.cif.gz | 26.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8his.ent.gz | 14.8 KB | Display | PDB format |
PDBx/mmJSON format | 8his.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8his_validation.pdf.gz | 395.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8his_full_validation.pdf.gz | 398.1 KB | Display | |
Data in XML | 8his_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 8his_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/8his ftp://data.pdbj.org/pub/pdb/validation_reports/hi/8his | HTTPS FTP |
-Related structure data
Related structure data | 8hu5C 8i50C 1i5wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 3184.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-CAD / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.22 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 10% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.040M Sodium cacodylate trihydrate pH 6.0, 0.012M Spermine tetrahydrochloride, 0.080M Potassium chloride, 0.020M Barium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→20.13 Å / Num. obs: 6474 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Χ2: 0.94 / Net I/σ(I): 55.1 |
Reflection shell | Resolution: 2.01→2.07 Å / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.055 / Num. measured all: 1890 / Num. unique obs: 294 / CC1/2: 0.998 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Χ2: 0.83 / Net I/σ(I) obs: 43.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I5W Resolution: 2.01→20.13 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.63 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→20.13 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|