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Yorodumi- PDB-122d: DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODEL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 122d | ||||||||||||||||||
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Title | DNA HELIX STRUCTURE AND REFINEMENT ALGORITHM: COMPARISON OF MODELS FOR D(CCAGGCM==5==CTGG) DERIVED FROM NUCLSQ, TNT, AND X-PLOR | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | Authors | Hahn, M. / Heinemann, U. | Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: DNA helix structure and refinement algorithm: comparison of models for d(CCAGGCm5CTGG) derived from NUCLSQ, TNT and X-PLOR. Authors: Hahn, M. / Heinemann, U. #1: Journal: J.Biol.Chem. / Year: 1992 Title: C-C-A-G-G-C-M5C-T-G-G: Helical Fine Structure, Hydration, and Comparison with C-C-A-G-G-C-C-T-G-G Authors: Heinemann, U. / Hahn, M. #2: Journal: Embo J. / Year: 1992 Title: Double Helix Conformation, Groove Dimensions and Ligand Binding Potential of a G/C-Stretch in B-DNA Authors: Heinemann, U. / Alings, C. / Bansal, M. #3: Journal: Embo J. / Year: 1991 Title: The Conformation of a B-DNA Decamer Is Mainly Determined by Its Sequence and Not by Crystal Environment Authors: Heinemann, U. / Alings, C. #4: Journal: J.Mol.Biol. / Year: 1989 Title: Crystallographic Study of One Turn of G/c-Rich B-DNA Authors: Heinemann, U. / Alings, C. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 122d.cif.gz | 23.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb122d.ent.gz | 13.9 KB | Display | PDB format |
PDBx/mmJSON format | 122d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 122d_validation.pdf.gz | 331.3 KB | Display | wwPDB validaton report |
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Full document | 122d_full_validation.pdf.gz | 358.2 KB | Display | |
Data in XML | 122d_validation.xml.gz | 5.5 KB | Display | |
Data in CIF | 122d_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/22/122d ftp://data.pdbj.org/pub/pdb/validation_reports/22/122d | 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 3060.020 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: 2.34 Å3/Da / Density % sol: 47.49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7.5 / Details: pH 7.50, MICRODIALYSIS, temperature 277.00K | |||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Details: Heinemann, U., (1991) Embo J., 10, 35. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
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Detector | Type: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.75 Å / Num. all: 7209 / Num. obs: 4704 |
Reflection | *PLUS Highest resolution: 1.7 Å |
-Processing
Software | Name: TNT / Classification: refinement | |||||||||||||||||||||
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Refinement | Resolution: 1.7→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.206 / Num. reflection obs: 3799 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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