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- PDB-3tar: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tar | |||||||||
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Title | Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-6) Position | |||||||||
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![]() | TRANSFERASE/DNA / DNA polymerase I / protein-DNA complex / TRANSFERASE-DNA complex | |||||||||
Function / homology | ![]() Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich ...Taq DNA Polymerase; Chain T, domain 4 / Taq DNA Polymerase; Chain T, domain 4 / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / Ribonuclease H-like superfamily/Ribonuclease H / DNA polymerase; domain 1 / Nucleotidyltransferase; domain 5 / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wang, W. / Beese, L.S. | |||||||||
![]() | ![]() Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Authors: Wang, W. / Hellinga, H.W. / Beese, L.S. #1: ![]() Title: Structures of mismatch replication errors observed in a DNA polymerase. Authors: Johnson, S.J. / Beese, L.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.8 KB | Display | ![]() |
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PDB format | ![]() | 219.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 29.7 KB | Display | |
Data in CIF | ![]() | 47 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pv8C ![]() 3px0C ![]() 3px4C ![]() 3px6C ![]() 3tanC ![]() 3tapC ![]() 3taqC ![]() 3thvC ![]() 3ti0C ![]() 1l3vS 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
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4554.962 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer Strand |
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#3: DNA chain | Mass: 4923.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template Strand |
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 67518.297 Da / Num. of mol.: 1 / Fragment: Bacillus Fragment (UNP residues 285-876) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Polysaccharide |
-Non-polymers , 3 types, 674 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE AUTHORS STATE THAT THE GEOBACILLU |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 45-50% saturated ammonium sulfate, 2.5% MPD, 10 mM magnesium sulfate, 100 mM MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 29, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→50 Å / Num. obs: 115264 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L3V Resolution: 1.6→45.295 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 2.35 / Phase error: 19.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.952 Å2 / ksol: 0.444 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→45.295 Å
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Refine LS restraints |
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LS refinement shell |
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