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Open data
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Basic information
Entry | Database: PDB / ID: 3qku | ||||||
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Title | Mre11 Rad50 binding domain in complex with Rad50 and AMP-PNP | ||||||
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Function / homology | ![]() DNA exonuclease activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Williams, G.J. / Williams, R.S. / Arvai, A. / Moncalian, G. / Tainer, J.A. | ||||||
![]() | ![]() Title: ABC ATPase signature helices in Rad50 link nucleotide state to Mre11 interface for DNA repair. Authors: Williams, G.J. / Williams, R.S. / Williams, J.S. / Moncalian, G. / Arvai, A.S. / Limbo, O. / Guenther, G. / Sildas, S. / Hammel, M. / Russell, P. / 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 | ![]() | 156.2 KB | Display | ![]() |
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PDB format | ![]() | 121.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3qkrC ![]() 3qksC ![]() 3qktC ![]() 1us8S C: citing same article ( S: Starting model for refinement |
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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: 41063.473 Da / Num. of mol.: 2 / Fragment: UNP residues 1-187, 716-882 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P58301, ![]() #2: Protein/peptide | | Mass: 4062.568 Da / Num. of mol.: 1 / Fragment: Rad50 binding domain (UNP residues 348-381) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8U1N9, ![]() #3: Chemical | #4: Chemical | Sequence details | THE RAD50 ABC-ATPASE CONSTRUCT CONSISTS OF UNP RESIDUES 1-187 AND 716-882 CONNECTED BY AN ...THE RAD50 ABC-ATPASE CONSTRUCT CONSISTS OF UNP RESIDUES 1-187 AND 716-882 CONNECTED BY AN ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.21 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100 mM Tris, 200-300 mM lithium sulfate, 12-13% PEG3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2007 |
Radiation | Monochromator: Kohzu Dual Double Crystal Monochromator (DDCM) Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.3→153.6 Å / Num. all: 18722 / Num. obs: 18667 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 3.301→3.387 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.6 / % possible all: 99.41 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1US8 Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU B: 32.231 / SU ML: 0.511 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.584 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.25 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 134.928 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.301→3.387 Å / Total num. of bins used: 20
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