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Yorodumi- PDB-4puq: Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4puq | ||||||
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Title | Mus Musculus Tdp2 reaction product complex with 5'-phosphorylated RNA/DNA, glycerol, and Mg2+ | ||||||
Components |
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Keywords | HYDROLASE/DNA/RNA / protein-DNA complex / DNA repair / 5'-DNA end processing / EEP domain / Hydrolase / Metalloenzyme / 5'-DNA end recognition / HYDROLASE-DNA-RNA complex | ||||||
Function / homology | Function and homology information tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / aggresome / neuron development / PML body / double-strand break repair / manganese ion binding ...tyrosyl-RNA phosphodiesterase activity / 5'-tyrosyl-DNA phosphodiesterase activity / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / phosphoric diester hydrolase activity / aggresome / neuron development / PML body / double-strand break repair / manganese ion binding / single-stranded DNA binding / endonuclease activity / nucleolus / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Schellenberg, M.J. / Williams, R.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Proteolytic Degradation of Topoisomerase II (Top2) Enables the Processing of Top2DNA and Top2RNA Covalent Complexes by Tyrosyl-DNA-Phosphodiesterase 2 (TDP2). Authors: Gao, R. / Schellenberg, M.J. / Huang, S.Y. / Abdelmalak, M. / Marchand, C. / Nitiss, K.C. / Nitiss, J.L. / Williams, R.S. / Pommier, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4puq.cif.gz | 287.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4puq.ent.gz | 230 KB | Display | PDB format |
PDBx/mmJSON format | 4puq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4puq_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
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Full document | 4puq_full_validation.pdf.gz | 465.4 KB | Display | |
Data in XML | 4puq_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 4puq_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/4puq ftp://data.pdbj.org/pub/pdb/validation_reports/pu/4puq | HTTPS FTP |
-Related structure data
Related structure data | 4gz1S S: Starting model for refinement |
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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
-Protein / DNA/RNA hybrid , 2 types, 4 molecules ABCD
#1: Protein | Mass: 28890.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tdp2, Ttrap / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9JJX7, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: DNA/RNA hybrid | Mass: 2731.799 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized nucleic acid |
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-Non-polymers , 4 types, 640 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 20% PEG 3350, 0.2M sodium acetate, 5mM MgCl2, pH 7.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. all: 84798 / Num. obs: 83186 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 18.99 Å2 / Rmerge(I) obs: 0.061 / Χ2: 0.993 / Net I/σ(I): 12 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GZ1 Resolution: 1.6→34.032 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8974 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 16.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.23 Å2 / Biso mean: 29.2718 Å2 / Biso min: 9.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→34.032 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: 29
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