+Open data
-Basic information
Entry | Database: PDB / ID: 6a46 | ||||||
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Title | Structure of TREX2 in complex with a nucleotide (dCMP) | ||||||
Components | Three prime repair exonuclease 2 | ||||||
Keywords | DNA BINDING PROTEIN / Exonuclease / DEDDh exonuclease | ||||||
Function / homology | Function and homology information exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / 3'-5'-DNA exonuclease activity / DNA metabolic process / molecular adaptor activity / DNA repair / magnesium ion binding / protein homodimerization activity / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hsiao, Y.Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: Structural insights into the duplex DNA processing of TREX2 Authors: Cheng, H.L. / Lin, C.T. / Huang, K.W. / Wang, S. / Lin, Y.T. / Toh, S.I. / Hsiao, Y.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a46.cif.gz | 267.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a46.ent.gz | 216.7 KB | Display | PDB format |
PDBx/mmJSON format | 6a46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/6a46 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/6a46 | HTTPS FTP |
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-Related structure data
Related structure data | 6a45C 6a47C 6a4bC 1y97S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28156.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Trex2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R1A9, exodeoxyribonuclease III #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #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: 1.86 Å3/Da / Density % sol: 33.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.02M Nickel(II) chloride hexahydrate, 0.02M Magnesium chloride hexahydrate, 0.02M Cadmium chloride hydrate, 0.1M Sodium acetate trihydrate pH 4.5, 24%(w/v) Polyethylene glycol monomethyl ether 2,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 27839 / % possible obs: 99.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.033 / Rsym value: 0.061 / Net I/σ(I): 22.37 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.875 / Num. unique obs: 2726 / Rpim(I) all: 0.344 / Rsym value: 0.589 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y97 Resolution: 2→28.859 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.859 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: 6.9973 Å / Origin y: 0.037 Å / Origin z: 21.2772 Å
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Refinement TLS group | Selection details: all |