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- PDB-1mu7: Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mu7 | ||||||
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Title | Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Tungstate Complex | ||||||
![]() | Tyrosyl-DNA Phosphodiesterase | ||||||
![]() | HYDROLASE / PLD Superfamily / Protein-Tungstate 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.J. | ||||||
![]() | ![]() 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. #1: ![]() Title: The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1 Authors: Davies, D.R. / Interthal, H. / Champoux, 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 | ![]() | 188.6 KB | Display | ![]() |
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PDB format | ![]() | 147.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.2 KB | Display | ![]() |
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Full document | ![]() | 476.9 KB | Display | |
Data in XML | ![]() | 35.1 KB | Display | |
Data in CIF | ![]() | 50 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mu9C ![]() 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 | The biological assembly is a monomer. There are two monomers per asymmetric unit, with the A monomer having the higher occupancy of bound tungstate. |
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Components
#1: Protein | Mass: 54731.195 Da / Num. of mol.: 2 / Fragment: RESIDUES 149-608 / Mutation: D322N,M328T,F548L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.47 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: PEG 8000, sodium chloride, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Feb 26, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.3 Å / Num. obs: 74158 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.58 % / Rsym value: 0.112 / Net I/σ(I): 9.24 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 2.18 / Rsym value: 0.409 / % possible all: 92.7 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 70186 / Rmerge(I) obs: 0.112 |
Reflection shell | *PLUS % possible obs: 92.7 % / Rmerge(I) obs: 0.409 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry 1jy1 Resolution: 2→46.3 Å / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The density is better defined for bound tungstate in the A subunit.
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Refinement step | Cycle: LAST / Resolution: 2→46.3 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 100 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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