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Yorodumi- PDB-4f1h: Crystal structure of TDP2 from Danio rerio complexed with a singl... -
+Open data
-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 | ||||||
Components |
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Keywords | Hydrolase/DNA / 5'-tyrosyl DNA phosphodiesterase / Hydrolase-DNA complex | ||||||
Function / homology | Function and homology information 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 ...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 | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.662 Å | ||||||
Authors | Shi, K. / Kurahashi, K. / Aihara, H. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f1h.cif.gz | 245.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f1h.ent.gz | 194.1 KB | Display | PDB format |
PDBx/mmJSON format | 4f1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/4f1h ftp://data.pdbj.org/pub/pdb/validation_reports/f1/4f1h | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Danio rerio (zebrafish) Gene: tdp2, ttrap, ttrapl, si:ch211-81e5.5, si:dkey-218n20.5 Production host: Escherichia coli (E. coli) 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.) Danio rerio (zebrafish) Gene: tdp2, ttrap, ttrapl, si:ch211-81e5.5, si:dkey-218n20.5 Production host: Escherichia coli (E. coli) References: UniProt: Q5XJA0, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
-Non-polymers , 4 types, 592 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.662→45.871 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 17.52 / Stereochemistry target values: ML
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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 |