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- PDB-1rgt: Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexe... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rgt | ||||||
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Title | Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC | ||||||
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![]() | HYDROLASE/DNA / Protein-DNA complex / vanadate complex / transition state mimic / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() 3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair ...3'-tyrosyl-DNA phosphodiesterase activity / single strand break repair / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / exonuclease activity / Nonhomologous End-Joining (NHEJ) / double-strand break repair / single-stranded DNA binding / double-stranded DNA binding / intracellular membrane-bounded organelle / DNA repair / nucleoplasm / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G. | ||||||
![]() | ![]() Title: Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes. Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G. #1: ![]() Title: Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide. Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J. #2: ![]() Title: Insights into substrate binding and catalytic mechanism of human Tyrosyl-DNA Phosphodiesterase (Tdp1) from vanadate and tungstate-inhibited structures Authors: Davies, D.R. / Interthal, H. / Champoux, J.J. / Hol, W.G.J. #3: ![]() Title: The crystal structure of human Tyrosyl-DNA Phosphodiesterase, Tdp1 Authors: Davies, D.R. / Interthal, H. / Campoux, J.J. / Hol, W.G.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 195.5 KB | Display | ![]() |
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PDB format | ![]() | 149.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rffC ![]() 1rfiC ![]() 1rg1C ![]() 1rg2C ![]() 1rguC ![]() 1rh0C ![]() 1jy1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | There are two biological assemblies per asymmetric unit--one composed of chains A and D, the other of chains B and F. |
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Components
-DNA chain / Protein , 2 types, 4 molecules DFAB
#1: DNA chain | Mass: 1190.830 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 54731.195 Da / Num. of mol.: 2 / Fragment: Residues 149-608 / Mutation: N322D, T328M, L548F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases |
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-Non-polymers , 5 types, 229 molecules ![](data/chem/img/VO4.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/OTS.gif)
![](data/chem/img/OTR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SPM.gif)
![](data/chem/img/OTS.gif)
![](data/chem/img/OTR.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SPM / | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: PEG 3000, NaCl, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 8.2 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 68032 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.15 % / Rsym value: 0.085 / Net I/σ(I): 15.29 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 3.38 / Rsym value: 0.368 / % possible all: 91.2 |
Reflection | *PLUS Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 91.2 % / Rmerge(I) obs: 0.368 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB structure 1JY1 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.724 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.713 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.228 / Rfactor Rwork: 0.196 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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