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Open data
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Basic information
Entry | Database: PDB / ID: 1kn0 | ||||||
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Title | Crystal Structure of the human Rad52 protein | ||||||
![]() | Rad52![]() | ||||||
![]() | ![]() ![]() ![]() | ||||||
Function / homology | ![]() double-strand break repair via single-strand annealing / DNA double-strand break processing involved in repair via single-strand annealing / DNA recombinase assembly / regulation of nucleotide-excision repair / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kagawa, W. / Kurumizaka, H. / Ishitani, R. / Fukai, S. / Nureki, O. / Shibata, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of the homologous-pairing domain from the human Rad52 recombinase in the undecameric form. Authors: Kagawa, W. / Kurumizaka, H. / Ishitani, R. / Fukai, S. / Nureki, O. / Shibata, T. / Yokoyama, 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 | ![]() | 356.7 KB | Display | ![]() |
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PDB format | ![]() | 301.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 23431.510 Da / Num. of mol.: 11 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.66 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 5000MME, ammonium sulfate, sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 27, 2001 | ||||||||||||
Radiation | Monochromator: DIAMOND / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.85→50 Å / Num. all: 63100 / Num. obs: 62872 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 | ||||||||||||
Reflection shell | Resolution: 2.85→2.9 Å / % possible all: 99.5 | ||||||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 63100 / Num. measured all: 1378830 / Rmerge(I) obs: 0.073 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 5.4 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor all![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.409 / Rfactor Rwork: 0.336 |