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Yorodumi- PDB-1d80: CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d80 | ||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MISMATCHED | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Skelly, J.V. / Edwards, K.J. / Jenkins, T.C. / Neidle, S. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 | Title: Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation. Authors: Skelly, J.V. / Edwards, K.J. / Jenkins, T.C. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d80.cif.gz | 26.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d80.ent.gz | 14.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d80_validation.pdf.gz | 371.1 KB | Display | wwPDB validaton report |
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Full document | 1d80_full_validation.pdf.gz | 392.9 KB | Display | |
Data in XML | 1d80_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 1d80_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/1d80 ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d80 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3703.416 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION, temperature 279.00K | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 279 K / pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.2 Å / Num. all: 8732 / Num. obs: 3811 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 14624 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(I): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(I): 2 / Num. reflection obs: 2365 / Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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