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Yorodumi- PDB-6q4u: KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q4u | ||||||
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Title | KlenTaq DNA pol in a closed ternary complex with 7-deaza-7-(2-(2-hydroxyethoxy)-N-(prop-2-yn-1-yl)acetamide)-2-dATP | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / DNA polymerase archaeal B-family modified nucleotide next-generation sequencing | ||||||
Function / homology | Function and homology information nucleoside binding / 5'-3' exonuclease activity / 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å | ||||||
Authors | Kropp, H.M. / Diederichs, K. / Marx, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2019 Title: The Structure of an Archaeal B-Family DNA Polymerase in Complex with a Chemically Modified Nucleotide. Authors: Kropp, H.M. / 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 | 6q4u.cif.gz | 377.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q4u.ent.gz | 308 KB | Display | PDB format |
PDBx/mmJSON format | 6q4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/6q4u ftp://data.pdbj.org/pub/pdb/validation_reports/q4/6q4u | HTTPS FTP |
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-Related structure data
Related structure data | 6q4tC 6q4vC 3rtvS 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: 61068.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: polA, pol1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19821, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 3601.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 4930.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 273 molecules
#4: Chemical | #5: Chemical | ChemComp-MN / | #6: Chemical | ChemComp-HHZ / [[( | #7: Chemical | #8: Chemical | ChemComp-GOL / | #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: 2.25 Å3/Da / Density % sol: 45.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 14 % PEG 8000, 0.1 M Tris pH 8.0, 0.2 M magnesium formate, 10 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.005→47.354 Å / Num. obs: 81414 / % possible obs: 99.9 % / Redundancy: 5.26 % / Rrim(I) all: 0.09 / Net I/σ(I): 11.21 |
Reflection shell | Resolution: 2.005→2.016 Å / Redundancy: 5.36 % / Mean I/σ(I) obs: 1.66 / Num. unique obs: 13148 / Rrim(I) all: 0.849 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RTV Resolution: 2.005→47.354 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 25
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.005→47.354 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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