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Open data
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Basic information
Entry | Database: PDB / ID: 3tho | ||||||
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Title | Crystal structure of Mre11:Rad50 in its ATP/ADP bound state | ||||||
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![]() | HYDROLASE/DNA BINDING PROTEIN / Adenosine Triphosphate / Bacterial Proteins / DNA Breaks / Double-Stranded / DNA Repair / DNA Repair Enzymes / DNA-Binding Proteins / Endodeoxyribonucleases / Exodeoxyribonucleases / Models / Molecular / Scattering / Small Angle / Thermotoga maritima / ABC ATPase / nuclease / HYDROLASE / HYDROLASE-DNA BINDING PROTEIN complex | ||||||
Function / homology | ![]() DNA exonuclease activity / Hydrolases; Acting on acid anhydrides / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / DNA recombination / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity ...DNA exonuclease activity / Hydrolases; Acting on acid anhydrides / 3'-5' exonuclease activity / DNA endonuclease activity / double-strand break repair / DNA recombination / DNA replication / Hydrolases; Acting on ester bonds / DNA repair / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moeckel, C. / Lammens, K. | ||||||
![]() | ![]() Title: ATP driven structural changes of the bacterial Mre11:Rad50 catalytic head complex. Authors: Mockel, C. / Lammens, K. / Schele, A. / Hopfner, K.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.5 KB | Display | ![]() |
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PDB format | ![]() | 130.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43077.074 Da / Num. of mol.: 1 Fragment: nucleotide binding domain, UNP residues 1-190 and 686-852 Mutation: D804C, H830C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 43973.297 Da / Num. of mol.: 1 / Fragment: UNP residues 7-385 / Mutation: H94Q, F291S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 6 types, 57 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ADP / | ||||||
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#4: Chemical | ChemComp-MG / | ||||||
#5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-PO4 / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.2 M ammonium sulfate 0.2 M ammonium L-tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 35646 / Observed criterion σ(I): 19.32 |
Reflection shell | Resolution: 2.6→2.61 Å / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.206 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6081→49.121 Å
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Refine LS restraints |
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LS refinement shell |
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