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Yorodumi- PDB-6dim: Crystal structure of Tdp1 catalytic domain in complex with Zenobi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dim | ||||||
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Title | Crystal structure of Tdp1 catalytic domain in complex with Zenobia fragment ZT1982 from cocktail soak | ||||||
Components | Tyrosyl-DNA phosphodiesterase 1 | ||||||
Keywords | hydrolase/hydrolase inhibitor / fragment-based drug design / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å | ||||||
Authors | Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Burke Jr., T.R. / Pommier, Y. / Waugh, D.S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening. Authors: Lountos, G.T. / Zhao, X.Z. / Kiselev, E. / Tropea, J.E. / Needle, D. / Pommier, Y. / Burke, T.R. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dim.cif.gz | 206.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dim.ent.gz | 162.8 KB | Display | PDB format |
PDBx/mmJSON format | 6dim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/6dim ftp://data.pdbj.org/pub/pdb/validation_reports/di/6dim | HTTPS FTP |
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-Related structure data
Related structure data | 6dhuC 6dieC 6dihC 6djdC 6djeC 6djfC 6djgC 6djhC 6djiC 6djjC 6mj5C 6n17C 6n19C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52126.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TDP1 / Production host: Escherichia coli (E. coli) References: UniProt: Q9NUW8, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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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: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M MOPS/HEPES-Na pH 7.5 10% w/v PEG 8000 20% v/v ethylene glycol 0.03M sodium fluoride 0.03M sodium bromide 0.03M sodium iodide |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. obs: 93819 / % possible obs: 97.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.036 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.82→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4647 / CC1/2: 0.622 / Rpim(I) all: 0.501 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Resolution: 1.81→40.988 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→40.988 Å
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Refine LS restraints |
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LS refinement shell |
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