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- PDB-1ub8: Crystal structure of d(GCGAAGC), bending duplex with a bulge-in r... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ub8 | ||||||||||||||||||
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Title | Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / sheared G:A pair / bulge-in duplex / G:AxA:G crossing | Function / homology | COBALT HEXAMMINE(III) / DNA | ![]() Method | ![]() ![]() ![]() ![]() Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A. | ![]() ![]() Title: Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing. Authors: Sunami, T. / Kondo, J. / Hirao, I. / Watanabe, K. / Miura, K. / Takenaka, A. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.8 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 393.3 KB | Display | ![]() |
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Full document | ![]() | 393.2 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 2147.437 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: chemically synthesized #2: Chemical | ChemComp-NCO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 43.92 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium cacodylate, sodium chloride, potassium chloride, hexaamminecobalt(III) chloride, MEGA-10, 2-methyl-2,4-pentanediol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 277 K / pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2000 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→24 Å / Num. all: 20712 / Num. obs: 20709 / % possible obs: 100 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 328413 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.6→24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å /
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.194 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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