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Open data
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Basic information
Entry | Database: PDB / ID: 4i29 | |||||||||
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Title | Binary complex of mouse TdT with ssDNA and Mn++ | |||||||||
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![]() | TRANSFERASE/DNA / Terminal transferase / TRANSFERASE-DNA complex | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gouge, J. / Delarue, M. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 176.7 KB | Display | ![]() |
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PDB format | ![]() | 135.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4i27C ![]() 4i28C ![]() 4i2aC ![]() 4i2bC ![]() 4i2cC ![]() 4i2dC ![]() 4i2eC ![]() 4i2fC ![]() 4i2gC ![]() 4i2hC ![]() 4i2iC ![]() 4i2jC ![]() 1jmsS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#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.) ![]() ![]() ![]() ![]() | ||||
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#2: DNA chain | Mass: 1598.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||||
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | PROTEIN FRAGMENT IS THE CATALYTIC CORE OF THE TDT-S (TDT-SMALL) ISOFORM (UNP RESIDUES 132-482, 503-530). | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20-26% PEG4000, 100 mM HEPES, 200 mM sodium chloride, 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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2012 |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9194 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.65 Å / Num. obs: 23982 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.87 Å2 / Rmerge(I) obs: 0.12 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3445 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JMS Resolution: 2.2→47.65 Å / Cor.coef. Fo:Fc: 0.9287 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.259 / SU Rfree Blow DPI: 0.195 / SU Rfree Cruickshank DPI: 0.185 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.236 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→47.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 12
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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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