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Yorodumi- PDB-1cgc: DOUBLE HELIX CONFORMATION GROOVE DIMENSIONS AND LIGAND BINDING PO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cgc | ||||||||||||||||||
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Title | DOUBLE HELIX CONFORMATION GROOVE DIMENSIONS AND LIGAND BINDING POTENTIAL OF A G/C-STRETCH IN B-DNA | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / B-DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | Authors | Heinemann, U. / Bansal, M. | Citation | 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. #1: Journal: J.Biol.Chem. / Year: 1992 Title: C-C-A-G-G-C-m5C-T-G-C: 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: 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. #3: 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 | 1cgc.cif.gz | 20.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cgc.ent.gz | 13.3 KB | Display | PDB format |
PDBx/mmJSON format | 1cgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cgc_validation.pdf.gz | 369.4 KB | Display | wwPDB validaton report |
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Full document | 1cgc_full_validation.pdf.gz | 380.8 KB | Display | |
Data in XML | 1cgc_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | 1cgc_validation.cif.gz | 5.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/1cgc ftp://data.pdbj.org/pub/pdb/validation_reports/cg/1cgc | 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: 3046.980 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: 2.06 Å3/Da / Density % sol: 40.25 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 7 / Details: pH 7.00, MICRODIALYSIS, 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 source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / 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: 2.2 Å / Num. all: 3078 / Num. obs: 2086 / Observed criterion σ(I): 1 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / % possible obs: 78 % / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.5 Å / % possible obs: 68 % |
-Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 2.2→8 Å / σ(F): 1 /
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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 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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