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Yorodumi- PDB-3rr8: Ternary Structure of the large fragment of Taq DNA polymerase bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rr8 | ||||||
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Title | Ternary Structure of the large fragment of Taq DNA polymerase bound to an abasic site and a ddGTP | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA polymerase / Abasic site / Translesion synthesis / A-rule / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information nucleoside binding / hydrolase activity, acting on ester bonds / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 3rr8.cif.gz | 247.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rr8.ent.gz | 194.3 KB | Display | PDB format |
PDBx/mmJSON format | 3rr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/3rr8 ftp://data.pdbj.org/pub/pdb/validation_reports/rr/3rr8 | HTTPS FTP |
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-Related structure data
Related structure data | 3rr7C 3rrgC 3rrhC 3t3fC 3lwlS 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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1 |
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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 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: 3657.395 Da / Num. of mol.: 1 / Fragment: DNA primer / Source method: obtained synthetically |
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#3: DNA chain | ( Mass: 4775.082 Da / Num. of mol.: 1 / Fragment: DNA template / Source method: obtained synthetically |
-Non-polymers , 3 types, 106 molecules
#4: Chemical | ChemComp-DG3 / | ||
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#5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M Na cacodylate pH 6.5, 0.2 M NH4OAc, 0.01 M Mg(OAc)2, 25% PEG 8000, 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: 1.0007 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2010 |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0007 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 213727 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.54 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 12.61 |
Reflection shell | Resolution: 2.38→2.53 Å / Redundancy: 8.01 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.61 / Num. unique all: 31236 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3LWL Resolution: 2.4→47.183 Å / SU ML: 0.36 / Isotropic thermal model: isotropic and tls / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.305 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze | Luzzati coordinate error obs: 0.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→47.183 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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