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Yorodumi- PDB-3taq: Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3taq | |||||||||
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Title | Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to Duplex DNA with Cytosine-Adenine Mismatch at (n-4) Position | |||||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase I / protein-DNA complex / TRANSFERASE-DNA complex | |||||||||
Function / homology | Function and homology information 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 | Geobacillus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | |||||||||
Authors | Wang, W. / Beese, L.S. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis. Authors: Wang, W. / Hellinga, H.W. / Beese, L.S. #1: Journal: Cell(Cambridge,Mass.) / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3taq.cif.gz | 276.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3taq.ent.gz | 216.1 KB | Display | PDB format |
PDBx/mmJSON format | 3taq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/3taq ftp://data.pdbj.org/pub/pdb/validation_reports/ta/3taq | HTTPS FTP |
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-Related structure data
Related structure data | 3pv8C 3px0C 3px4C 3px6C 3tanC 3tapC 3tarC 3thvC 3ti0C 1l5uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3961.588 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.) Geobacillus (bacteria) / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C9RTX7, DNA-directed DNA polymerase |
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#4: Polysaccharide |
-Non-polymers , 3 types, 780 molecules
#5: Chemical | ChemComp-MG / | ||
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#6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
-Details
Sequence details | THE AUTHORS STATE THAT THE GEOBACILLU |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.38 % |
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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: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97121 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2009 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97121 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 101635 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.046 / Net I/σ(I): 21.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1L5U Resolution: 1.65→40.784 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 2.35 / Phase error: 17.91 / 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: 48.81 Å2 / ksol: 0.449 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.65→40.784 Å
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Refine LS restraints |
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LS refinement shell |
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