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Yorodumi- PDB-5ink: Mouse Tdp2 reaction product (5'-phosphorylated DNA)-abasic/THF-Mg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ink | ||||||
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Title | Mouse Tdp2 reaction product (5'-phosphorylated DNA)-abasic/THF-Mg2+ complex | ||||||
Components |
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Keywords | hydrolase/dna / hydrolase / dna repair / endonuclease/exonuclease/phosphatase (EEP) domain / hydrolase-dna 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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Schellenberg, M.J. / Williams, R.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2016 Title: Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Authors: Schellenberg, M.J. / Perera, L. / Strom, C.N. / Waters, C.A. / Monian, B. / Appel, C.D. / Vilas, C.K. / Williams, J.G. / Ramsden, D.A. / Williams, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ink.cif.gz | 248.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ink.ent.gz | 194.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ink.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/5ink ftp://data.pdbj.org/pub/pdb/validation_reports/in/5ink | HTTPS FTP |
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-Related structure data
Related structure data | 5ht2C 5inlC 5inmC 5innC 5inoC 5inpC 5inqC 4gz1S 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
-Protein / DNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 28905.230 Da / Num. of mol.: 2 / Fragment: unp residues 118-370 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 chain | Mass: 2606.713 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 5 types, 446 molecules
#3: Chemical | ChemComp-GOL / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-EPE / | #6: Chemical | ChemComp-PEG / | #7: 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: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG3350, 200mM NaOAc, 20 mM Magnesium formate, 100 mM HEPES |
-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: RAYONIX MX300-HS / Detector: CCD / Date: Jul 1, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 34435 / % possible obs: 98.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.899 Å2 / Rmerge(I) obs: 0.125 / Net I/av σ(I): 14.583 / Net I/σ(I): 8.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GZ1 Resolution: 2.15→45.68 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso max: 160.11 Å2 / Biso mean: 36.5319 Å2 / Biso min: 2.01 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→45.68 Å
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