+Open data
-Basic information
Entry | Database: PDB / ID: 3dsc | ||||||
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Title | Crystal structure of P. furiosus Mre11 DNA synaptic complex | ||||||
Components |
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Keywords | Hydrolase/DNA / Protein-DNA complex / Double Helix / Nuclease / DNA damage / DNA repair / Endonuclease / Exonuclease / Hydrolase / Manganese / Metal-binding / Hydrolase-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA end binding / Y-form DNA binding / 3'-5' exonuclease activity / double-strand break repair / manganese ion binding / endonuclease activity / Hydrolases; Acting on ester bonds / identical protein binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Williams, R.S. / Moncalian, G. / Shin, D.S. / Tainer, J.A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2008 Title: Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair. Authors: Williams, R.S. / Moncalian, G. / Williams, J.S. / Yamada, Y. / Limbo, O. / Shin, D.S. / Groocock, L.M. / Cahill, D. / Hitomi, C. / Guenther, G. / Moiani, D. / Carney, J.P. / Russell, P. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dsc.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dsc.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 3dsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/3dsc ftp://data.pdbj.org/pub/pdb/validation_reports/ds/3dsc | HTTPS FTP |
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-Related structure data
Related structure data | 3dsdC 1ii7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40920.660 Da / Num. of mol.: 1 / Fragment: pfMre11 Nuclease domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: mre11, PF1166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1N9 |
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#2: DNA chain | Mass: 6099.952 Da / Num. of mol.: 1 / Fragment: 3' overhang DNA hairpin / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.22 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 1000, 0.1 M Tris-HCl, 0.2 M MgCl2, 0.2 M 1,6 hexanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 10769 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1II7 Resolution: 2.7→19.94 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.877 / SU B: 32.169 / SU ML: 0.329 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.368 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.9472 Å / Origin y: 6.5159 Å / Origin z: 18.1059 Å
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Refinement TLS group |
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