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Open data
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Basic information
Entry | Database: PDB / ID: 1ue4 | ||||||||||||||||||
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Title | Crystal structure of d(GCGAAAGC) | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / sheared G:A pair / bulge-in duplex / G:AxA:G crossing | Function / homology | 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 | ![]() | 15 KB | Display | ![]() |
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PDB format | ![]() | 9.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 343.7 KB | Display | ![]() |
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Full document | ![]() | 343.7 KB | Display | |
Data in XML | ![]() | 3 KB | Display | |
Data in CIF | ![]() | 3.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ub8C ![]() 1ue2S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 2460.644 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.55 Å3/Da / Density % sol: 19.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: sodium chloride, magnesium chloride, spermine 4HCl, 2-methyl-2,4-pentanediol, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 277 K / 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: Oct 21, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→26 Å / Num. all: 3177 / Num. obs: 3175 / % possible obs: 99.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 88780 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 100 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UE2 Resolution: 1.65→15 Å / σ(F): 3 Stereochemistry target values: G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64
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Refinement step | Cycle: LAST / Resolution: 1.65→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å /
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.209 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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