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Yorodumi- PDB-3t3f: Ternary Structure of the large fragment of Taq DNA polymerase bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t3f | ||||||
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Title | Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and dNITP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / Abasic site / Translesion synthesis / A-rule / base stacking / dNITP / Nitroindol triphosphate / base analogue / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information nucleoside binding / hydrolase activity, acting on ester bonds / double-strand break repair via alternative nonhomologous end joining / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Marx, A. / Diederichs, K. / Obeid, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Amino acid templating mechanisms in selection of nucleotides opposite abasic sites by a family a DNA polymerase. Authors: Obeid, S. / Welte, W. / Diederichs, K. / Marx, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t3f.cif.gz | 269.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t3f.ent.gz | 211.6 KB | Display | PDB format |
PDBx/mmJSON format | 3t3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t3f_validation.pdf.gz | 790 KB | Display | wwPDB validaton report |
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Full document | 3t3f_full_validation.pdf.gz | 808.8 KB | Display | |
Data in XML | 3t3f_validation.xml.gz | 28 KB | Display | |
Data in CIF | 3t3f_validation.cif.gz | 39.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/3t3f ftp://data.pdbj.org/pub/pdb/validation_reports/t3/3t3f | HTTPS FTP |
-Related structure data
Related structure data | 3rr7C 3rr8C 3rrgC 3rrhC 3ktqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 60936.965 Da / Num. of mol.: 1 / Fragment: klenow fragment (UNP residues 293-832) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: pol I, pol1, polA / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P19821, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3617.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA primer |
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#3: DNA chain | Mass: 4815.106 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA template |
-Non-polymers , 6 types, 341 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-NA / | #7: Chemical | ChemComp-N5P / | #8: Chemical | ChemComp-FMT / #9: Water | ChemComp-HOH / | |
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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: 2.29 Å3/Da / Density % sol: 46.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M TRIS HCl, 0.2 M MgFormate, 18% PEG 8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2011 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 50729 / Num. obs: 50510 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.9→2.01 Å / Rmerge(I) obs: 0.935 / Mean I/σ(I) obs: 1.58 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KTQ Resolution: 1.9→42.155 Å / SU ML: 0.52 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 19.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.52 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→42.155 Å
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Refine LS restraints |
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LS refinement shell |
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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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