+Open data
-Basic information
Entry | Database: PDB / ID: 4fva | ||||||
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Title | Crystal structure of truncated Caenorhabditis elegans TDP2 | ||||||
Components | 5'-tyrosyl-DNA phosphodiesterase | ||||||
Keywords | HYDROLASE / 5'-phosphotyrosyl-DNA diesterase | ||||||
Function / homology | Function and homology information 5'-tyrosyl-DNA phosphodiesterase activity / nuclease activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / PML body / double-strand break repair / single-stranded DNA binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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 | 4fva.cif.gz | 431 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fva.ent.gz | 354.7 KB | Display | PDB format |
PDBx/mmJSON format | 4fva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/4fva ftp://data.pdbj.org/pub/pdb/validation_reports/fv/4fva | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 29283.492 Da / Num. of mol.: 4 / Fragment: unp residues 107-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Y63D3A.4 / Production host: Escherichia coli (E. coli) References: UniProt: Q9XWG3, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-MLI / #5: 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: 1.99 Å3/Da / Density % sol: 38.05 % |
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Crystal grow | Temperature: 293 K / pH: 5 Details: 30% PEG 3,350 and 0.2M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 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 10, 2011 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 66104 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 14.16 |
Reflection shell | Resolution: 1.95→1.98 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.566 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→44.993 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 22.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→44.993 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: 13.4368 Å / Origin y: 1.3072 Å / Origin z: -20.5082 Å
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Refinement TLS group | Selection details: all |