+Open data
-Basic information
Entry | Database: PDB / ID: 3av0 | ||||||
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Title | Crystal structure of Mre11-Rad50 bound to ATP S | ||||||
Components | (DNA double-strand break repair ...) x 2 | ||||||
Keywords | RECOMBINATION / DNA repair / Calcineurin-like phosphoesterase / ABC transporter ATPase domain-like / DNA double-strand break repair / HerA-NurA complex / Nbs1 in eukaryotes | ||||||
Function / homology | Function and homology information DNA exonuclease activity / 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 / DNA repair / ATP hydrolysis activity ...DNA exonuclease activity / 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 / DNA repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Lim, H.S. / Kim, J.S. / Cho, Y. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Mre11-Rad50-ATP S Complex: Understanding the Interplay between Mre11 and Rad50 Authors: Lim, H.S. / Kim, J.S. / Park, Y.B. / Gwon, G.H. / Cho, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3av0.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3av0.ent.gz | 129.8 KB | Display | PDB format |
PDBx/mmJSON format | 3av0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3av0_validation.pdf.gz | 761 KB | Display | wwPDB validaton report |
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Full document | 3av0_full_validation.pdf.gz | 811.1 KB | Display | |
Data in XML | 3av0_validation.xml.gz | 34 KB | Display | |
Data in CIF | 3av0_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/3av0 ftp://data.pdbj.org/pub/pdb/validation_reports/av/3av0 | HTTPS FTP |
-Related structure data
Related structure data | 3auySC 3auzC 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
-DNA double-strand break repair ... , 2 types, 2 molecules AB
#1: Protein | Mass: 45370.930 Da / Num. of mol.: 1 / Fragment: Nuclease domain (UNP RESIDUES 1-313) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: rad50, MJ1322 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q58719 |
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#2: Protein | Mass: 42389.930 Da / Num. of mol.: 1 / Fragment: ABC ATPase domain (UNP RESIDUES 1-190, 825-1005) Source method: isolated from a genetically manipulated source Details: The fusion protein of residues 1-190 and residues 825-1005 Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: rad50, MJ1322 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58718 |
-Non-polymers , 6 types, 30 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-AGS / | #7: Chemical | ChemComp-MG / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10 % PEG 3350, 0.1M ADA pH6.2, 0.1M Lithium sulfate, 2% iso-propanol, 5% Acetonitrile , 1mM ATP, 5mM magnessium chloride , VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2010 |
Radiation | Monochromator: Si 4-channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 20290 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.1→3.15 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1II7, 3AUY Resolution: 3.1→29.318 Å / SU ML: 0.4 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.401 Å2 / ksol: 0.291 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.1→29.318 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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