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- PDB-4ztz: Structural basis for processivity and antiviral drug toxicity in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ztz | ||||||
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Title | Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase | ||||||
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![]() | DNA Binding Protein/DNA / ![]() ![]() | ||||||
Function / homology | ![]() gamma DNA polymerase complex / mitochondrial DNA replication / positive regulation of DNA-directed DNA polymerase activity / single-stranded DNA 3'-5' DNA exonuclease activity / DNA replication proofreading / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Szymanski, M.R. / Yin, Y.W. | ||||||
![]() | ![]() Title: Structural basis for processivity and antiviral drug toxicity in human mitochondrial DNA replicase Authors: Szymanski, M.R. / Kuznestov, V.B. / Shumate, C.K. / Meng, Q. / Lee, Y.-S. / Patel, G. / Patel, S.S. / Yin, Y.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 391.8 KB | Display | ![]() |
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PDB format | ![]() | 300.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
-DNA polymerase subunit gamma- ... , 2 types, 3 molecules ABC
#1: Protein | ![]() Mass: 138037.703 Da / Num. of mol.: 1 / Fragment: UNP residues 30-1239 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P54098, ![]() |
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#2: Protein | ![]() Mass: 53655.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9UHN1 |
-DNA chain , 2 types, 2 molecules TP
#3: DNA chain | Mass: 8235.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 7421.821 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 2 types, 3 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/DCP.gif)
![](data/chem/img/DCP.gif)
#5: Chemical | #6: Chemical | ChemComp-DCP / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68.31 % |
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Crystal grow![]() | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: PEG8000, KCl, CaCl2 / PH range: 5.5-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.442→48.5 Å / Num. obs: 48718 / % possible obs: 99.6 % / Redundancy: 5.8 % / Net I/σ(I): 2 |
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Processing
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Refinement | Resolution: 3.442→45.5 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.33 / 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: 3.442→45.5 Å
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Refine LS restraints |
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LS refinement shell |
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