+Open data
-Basic information
Entry | Database: PDB / ID: 4i2e | ||||||
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Title | Ternary complex of mouse TdT with ssDNA and AMPcPP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Terminal transferase / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gouge, J. / Delarue, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism. Authors: Gouge, J. / Rosario, S. / Romain, F. / Beguin, P. / Delarue, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i2e.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i2e.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 4i2e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/4i2e ftp://data.pdbj.org/pub/pdb/validation_reports/i2/4i2e | HTTPS FTP |
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-Related structure data
Related structure data | 4i27C 4i28C 4i29C 4i2aC 4i2bC 4i2cC 4i2dC 4i2fC 4i2gC 4i2hC 4i2iC 4i2jC 1jmsS 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
-Protein / DNA chain , 2 types, 2 molecules AC
#1: Protein | Mass: 45704.008 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt, Tdt / Production host: Escherichia coli (E. coli) / References: UniProt: P09838, DNA nucleotidylexotransferase |
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#2: DNA chain | Mass: 1521.077 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 408 molecules
#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-APC / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | PROTEIN FRAGMENT IS THE CATALYTIC CORE OF THE TDT-S (TDT-SMALL) ISOFORM (UNP RESIDUES 132-482, 503-530). |
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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: 2.46 Å3/Da / Density % sol: 49.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20-26% PEG4000, 100 mM HEPES, 200 mM ammonium acetate, pH 6.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 6.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9196 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2012 |
Radiation | Monochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 2→48 Å / Num. obs: 31783 / % possible obs: 98.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 34.09 Å2 / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.705 / Mean I/σ(I) obs: 2 / Num. unique all: 4628 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JMS Resolution: 2→42.39 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.9143 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.155 / SU Rfree Cruickshank DPI: 0.147 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.253 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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