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Yorodumi- PDB-1d60: THE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: TRIGONAL FORM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d60 | ||||||||||||||||||
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Title | THE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: TRIGONAL FORM | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX / MODIFIED | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Lipanov, A. / Kopka, M.L. / Kaczor-Grzeskowiak, M. / Quintana, J. / Dickerson, R.E. | Citation | Journal: Biochemistry / Year: 1993 | Title: Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA. Authors: Lipanov, A. / Kopka, M.L. / Kaczor-Grzeskowiak, M. / Quintana, J. / 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 | 1d60.cif.gz | 21.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d60.ent.gz | 13.1 KB | Display | PDB format |
PDBx/mmJSON format | 1d60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d60_validation.pdf.gz | 367.7 KB | Display | wwPDB validaton report |
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Full document | 1d60_full_validation.pdf.gz | 380.5 KB | Display | |
Data in XML | 1d60_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1d60_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/1d60 ftp://data.pdbj.org/pub/pdb/validation_reports/d6/1d60 | 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: 3029.990 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 248 K |
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Diffraction source | Source: ROTATING ANODE |
Detector | Type: RIGAKU AFC-5R / Detector: DIFFRACTOMETER |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→8 Å / Num. all: 3202 / Num. obs: 1725 / Observed criterion σ(I): 2 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Observed criterion σ(I): 2 / Num. measured all: 3202 |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(F): 2 /
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Refine Biso |
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 2 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |