+Open data
-Basic information
Entry | Database: PDB / ID: 3dnb | |||||||||||||||||||||
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Title | HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER | |||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MISMATCHED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.3 Å | Authors | Prive, G.G. / 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. #1: Journal: Science / Year: 1987 Title: Helix Geometry, Hydration, and G.A Mismatch in a B-DNA Decamer Authors: Prive, G.G. / Heinemann, U. / Chandrasegaran, S. / Kan, L.S. / Kopka, M.L. / Dickerson, R.E. #2: Journal: Structure and Expression / Year: 1988 Title: A Mismatch Decamer as a Model for General-Sequence B-DNA Authors: Prive, G.G. / Heinemann, U. / Chandrasegaran, S. / Kan, L.-S. / Kopka, M.L. / 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 | 3dnb.cif.gz | 18.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dnb.ent.gz | 10.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dnb_validation.pdf.gz | 358.6 KB | Display | wwPDB validaton report |
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Full document | 3dnb_full_validation.pdf.gz | 363.3 KB | Display | |
Data in XML | 3dnb_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 3dnb_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/3dnb ftp://data.pdbj.org/pub/pdb/validation_reports/dn/3dnb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3069.030 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K | ||||||||||||||||||||||||||||||||||||
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 | Ambient temp details: ROOM TEMPERATURE |
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Detector | Type: NICOLET P1 / Detector: DIFFRACTOMETER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.3→8 Å |
Reflection | *PLUS |
-Processing
Software | Name: NUCLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.3→8 Å / Occupancy max: 1 / Occupancy min: 0.53 / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 1.3→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.3 Å / Lowest resolution: 8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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