+
Open data
-
Basic information
Entry | Database: PDB / ID: 4i2d | ||||||
---|---|---|---|---|---|---|---|
Title | Binary complex of mouse TdT with AMPcPP | ||||||
![]() | DNA nucleotidylexotransferase | ||||||
![]() | TRANSFERASE / Terminal transferase | ||||||
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 95.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 760.4 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4i27C ![]() 4i28C ![]() 4i29C ![]() 4i2aC ![]() 4i2bC ![]() 4i2cC ![]() 4i2eC ![]() 4i2fC ![]() 4i2gC ![]() 4i2hC ![]() 4i2iC ![]() 4i2jC ![]() 1jmsS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#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.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 266 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/APC.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MG / |
---|---|
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-APC / |
#5: Chemical | ChemComp-ZN / |
#6: Water | ChemComp-HOH / |
-Details
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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.15 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2012 |
Radiation | Monochromator: channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.915 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47 Å / Num. obs: 20328 / % possible obs: 98.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 45.65 Å2 / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2 / Num. unique all: 2936 / % possible all: 99 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JMS Resolution: 2.3→23.93 Å / Cor.coef. Fo:Fc: 0.8851 / Cor.coef. Fo:Fc free: 0.8756 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.334 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.214 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.88 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.308 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→23.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.42 Å / Total num. of bins used: 10
|