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Yorodumi- PDB-5dnb: STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dnb | |||||||||||||||||||||
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Title | STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-G-T-T-G-G AND COMPARISON WITH ISOMORPHOUS DECAMERS C-C-A-A-G-A-T-T-G-G AND C-C-A-G-G-C-C-T-G-G | |||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.4 Å | Authors | Prive, G.G. / Yanagi, K. / Dickerson, R.E. | Citation | Journal: J.Mol.Biol. / Year: 1991 | Title: Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. Authors: Prive, G.G. / Yanagi, K. / Dickerson, R.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dnb.cif.gz | 18.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dnb.ent.gz | 10.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/5dnb ftp://data.pdbj.org/pub/pdb/validation_reports/dn/5dnb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THESE WATER MOLECULES MAKE A SPLINE OF HYDRATION. / 2: THESE WATER MOLECULES MAKE A SPLINE OF HYDRATION. / 3: THESE WATER MOLECULES MAKE A SPLINE OF HYDRATION. / 4: HOH 63 IS ONLY 1.57 ANGSTROMS FROM THE O4* OF A 8. | ||||||||
Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | ChemComp-MG / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.91 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / Details: VAPOR DIFFUSION | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.4→8 Å / Num. obs: 4402 / Observed criterion σ(I): 1 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.4→8 Å / σ(F): 1 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.4→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.4 Å / Num. reflection all: 4402 / σ(F): 1 / Rfactor all: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |