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- PDB-6dt1: Crystal structure of the ligase from bacteriophage T4 complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6dt1 | |||||||||
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Title | Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate | |||||||||
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![]() | LIGASE/DNA / LIGASE-DNA COMPLEX / LIGASE | |||||||||
Function / homology | ![]() DNA ligase activity / DNA ligase (ATP) / DNA ligase (ATP) activity / DNA recombination / DNA replication / DNA repair / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shi, K. / Aihara, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: T4 DNA ligase structure reveals a prototypical ATP-dependent ligase with a unique mode of sliding clamp interaction. Authors: Shi, K. / Bohl, T.E. / Park, J. / Zasada, A. / Malik, S. / Banerjee, S. / Tran, V. / Li, N. / Yin, Z. / Kurniawan, F. / Orellana, K. / Aihara, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 450.5 KB | Display | ![]() |
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PDB format | ![]() | 361.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 40.1 KB | Display | |
Data in CIF | ![]() | 56.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wfyC ![]() 6drtC ![]() 1x9nS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AE
#1: Protein | Mass: 57540.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 3 types, 6 molecules BFCGDH
#2: DNA chain | Mass: 3349.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: DNA chain | Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #4: DNA chain | Mass: 6393.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 7 types, 290 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/AMP.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-1PE / | #7: Chemical | ChemComp-DTT / #8: Chemical | #9: Chemical | ChemComp-MG / | #10: Chemical | #11: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350 / PH range: 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→113.572 Å / Num. obs: 42792 / % possible obs: 98.6 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4259 / CC1/2: 0.622 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1x9n Resolution: 2.75→113.021 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.5 / 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: 2.75→113.021 Å
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Refine LS restraints |
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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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