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- PDB-3pv8: 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: 3pv8 | ||||||
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Title | Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation | ||||||
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![]() | TRANSFERASE/DNA / DNA Polymerase I / protein-DNA complex / Thymine-Adenine / closed conformation / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 530 KB | Display | ![]() |
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PDB format | ![]() | 428.6 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 | ![]() | 62.4 KB | Display | |
Data in CIF | ![]() | 98.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3px0C ![]() 3px4C ![]() 3px6C ![]() 3tanC ![]() 3tapC ![]() 3taqC ![]() 3tarC ![]() 3thvC ![]() 3ti0C ![]() 2hviS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 67490.289 Da / Num. of mol.: 2 Fragment: Bacillus Fragment (analogous to E. coli Klenow Fragment) Mutation: D598A, F710Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 2 types, 4 molecules BECF
#2: DNA chain | Mass: 2650.762 Da / Num. of mol.: 2 / Fragment: DNA primer strand / Source method: obtained synthetically #3: DNA chain | Mass: 4024.649 Da / Num. of mol.: 2 / Fragment: DNA template strand / Source method: obtained synthetically |
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-Non-polymers , 4 types, 1830 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/D3T.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/D3T.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLUS SPECIES WHOSE SEQUENCE IS ...AUTHORS STATE THAT THE PROTEIN WAS ISOLATED FROM A STRAIN OF GEOBACILLU |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: Ammonium Sulfate, MPD, MgSO4, MES, pH 5.8, vapor diffusion, hanging drop, temperature 290K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97121 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→100 Å / Num. obs: 231085 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.94 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2HVI with insertion site base pair, metal ions, and protein residues 681-727 deleted. Resolution: 1.52→88.422 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.36 / σ(F): 2.35 / Phase error: 19.45 / 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: 44.623 Å2 / ksol: 0.411 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.52→88.422 Å
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Refine LS restraints |
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LS refinement shell |
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