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- PDB-4f1h: Crystal structure of TDP2 from Danio rerio complexed with a singl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f1h | ||||||
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Title | Crystal structure of TDP2 from Danio rerio complexed with a single strand DNA | ||||||
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![]() | Hydrolase/DNA / 5'-tyrosyl DNA phosphodiesterase / Hydrolase-DNA complex | ||||||
Function / homology | ![]() tyrosyl-DNA phosphodiesterase activity / convergent extension involved in gastrulation / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / determination of left/right symmetry / gastrulation / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / double-strand break repair ...tyrosyl-DNA phosphodiesterase activity / convergent extension involved in gastrulation / 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / determination of left/right symmetry / gastrulation / negative regulation of transforming growth factor beta receptor signaling pathway / PML body / double-strand break repair / single-stranded DNA binding / manganese ion binding / magnesium ion binding / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shi, K. / Kurahashi, K. / Aihara, H. | ||||||
![]() | ![]() Title: Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2. Authors: Shi, K. / Kurahashi, K. / Gao, R. / Tsutakawa, S.E. / Tainer, J.A. / Pommier, Y. / Aihara, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.8 KB | Display | ![]() |
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PDB format | ![]() | 194.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.1 KB | Display | ![]() |
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Full document | ![]() | 466.8 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA chain , 1 types, 1 molecules C
#1: DNA chain | Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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-Tyrosyl-DNA phosphodiesterase ... , 2 types, 2 molecules AB
#2: Protein | Mass: 28484.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: tdp2, ttrap, ttrapl, si:ch211-81e5.5, si:dkey-218n20.5 Production host: ![]() ![]() References: UniProt: Q5XJA0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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#3: Protein | Mass: 28613.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: tdp2, ttrap, ttrapl, si:ch211-81e5.5, si:dkey-218n20.5 Production host: ![]() ![]() References: UniProt: Q5XJA0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
-Non-polymers , 4 types, 592 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PO4 / | ||||
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#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | A LARGE PORTION OF THE N-TERMINAL WAS NOT OBSERVED IN THE ELECTRON DENSITY |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % |
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Crystal grow | Temperature: 293 K / pH: 7 Details: PEG and sodium tartrate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 96 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2011 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→50 Å / Num. obs: 67804 / % possible obs: 99.4 % / Observed criterion σ(I): 0 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.239 Å2 / ksol: 0.353 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.662→45.871 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.7302 Å / Origin y: -2.4536 Å / Origin z: -1.7162 Å
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Refinement TLS group | Selection details: all |