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- PDB-4o43: DNA Double-Strand Break Repair Pathway Choice Is Directed by Dist... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4o43 | |||||||||
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Title | DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities | |||||||||
![]() | Exonuclease, putative | |||||||||
![]() | DNA BINDING PROTEIN/inhibitor / DNA repair DNA double-strand break repair thermophilic MRE11 nuclease / DNA repair DNA double-strand break repair / DNA BINDING PROTEIN-inhibitor complex | |||||||||
Function / homology | ![]() DNA exonuclease activity / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / DNA recombination / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / DNA binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M. / Maity, R. / Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. ...Shibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M. / Maity, R. / Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. / Ismail, A. / Ismalaj, E. / Petricci, E. / Neale, M.J. / Bristow, R.G. / Masson, J. / Wyman, C. / Jeggo, P.A. / Tainer, J.A. | |||||||||
![]() | ![]() Title: DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities. Authors: Shibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M.M. / Maity, R. / van Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. / Ismail, A. / Ismalaj, E. / Petricci, E. ...Authors: Shibata, A. / Moiani, D. / Arvai, A.S. / Perry, J. / Harding, S.M. / Genois, M.M. / Maity, R. / van Rossum-Fikkert, S. / Kertokalio, A. / Romoli, F. / Ismail, A. / Ismalaj, E. / Petricci, E. / Neale, M.J. / Bristow, R.G. / Masson, J.Y. / Wyman, C. / Jeggo, P.A. / Tainer, J.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 | ![]() | 275.7 KB | Display | ![]() |
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PDB format | ![]() | 222.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1007 KB | Display | ![]() |
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Full document | ![]() | 1017.6 KB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nzvSC ![]() 4o24C ![]() 4o4kC ![]() 4o5gC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38575.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.81 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion / pH: 6 / Details: pH 6, VAPOR DIFFUSION, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 32631 / Num. obs: 32631 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NZV Resolution: 2.4→37.88 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 28.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→37.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 17.4074 Å / Origin y: 456.3056 Å / Origin z: 20.0226 Å
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Refinement TLS group | Selection details: all |