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- PDB-1p4y: Effect of Sequence on the Conformational Geometry of DNA Holliday... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p4y | ||||||||||||||||||
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Title | Effect of Sequence on the Conformational Geometry of DNA Holliday Junctions | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / Holliday Junction / DNA Four-Way Junction | Function / homology | DNA | ![]() Method | ![]() ![]() ![]() Hays, F.A. / Vargason, J.M. / Ho, P.S. | ![]() ![]() Title: Effect of Sequence on the Conformation of DNA Holliday Junctions Authors: Hays, F.A. / Vargason, J.M. / Ho, P.S. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 21.9 KB | Display | ![]() |
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PDB format | ![]() | 14.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 383.9 KB | Display | ![]() |
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Full document | ![]() | 384.5 KB | Display | |
Data in XML | ![]() | 4.1 KB | Display | |
Data in CIF | ![]() | 5.6 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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Unit cell |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS A AND B. THE FULL FOUR STRANDED HOLLIDAY JUNCTION STRUCTURE CAN BE GENERATED BY THE FOLLOWING: matrix= ( -1.00000 -0.00046 -0.00015 ) ( -0.00046 1.00000 0.00072 ) ( 0.00015 0.00072 -1.00000 ) translation= (-12.65734 -0.02663 34.77174) |
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Components
#1: DNA chain | Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC ...Details: DNA was synthesized on an Applied Biosystems DNA synthesizer using phosphoramidite chemistry, with the trityl-protecting group left intact at the 5-terminal nucleotide, FOR SUBSEQUENT HPLC PURIFICATION, THEN DEPROTECTED BY TREATMENT WITH 3% ACETIC ACID FOR FIFTEEN MINUTES, NEUTRALIZED WITH AMMONIUM HYDROXIDE, AND DESALTED ON A SIGMA G-25 SEPHADEX COLUMN. #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 35.95 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / pH: 7 Details: 0.5mM DNA, 25mM sodium cacodylate, 7.5mM CaCl2, 0.1mM SPERMINE TETRAHYDROCHLORIDE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 7.00 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2003 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→22.55 Å / Num. obs: 4940 / % possible obs: 74 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 1.6 Å2 / Rmerge(I) obs: 0.048 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 2.14 / % possible all: 21.7 |
Reflection | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 50 Å / Num. obs: 5137 / % possible obs: 78.7 % / Rmerge(I) obs: 0.049 / Num. measured all: 50581 |
Reflection shell | *PLUS % possible obs: 48 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 2.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: UD0008 Resolution: 1.7→22.5 Å / Rfactor Rfree error: 0.012 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 8.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→22.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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