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Yorodumi- PDB-6is7: Structure of 9N-I DNA polymerase incorporation with dA in the act... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6is7 | ||||||
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Title | Structure of 9N-I DNA polymerase incorporation with dA in the active site | ||||||
Components |
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Keywords | TRANSFERASE/DNA / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | Thermococcus sp. 9oN-7 (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Linwu, S.W. / Maestre-Reyna, M. / Tsai, M.D. / Tu, Y.H. / Chang, W.H. | ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing. Authors: LinWu, S.W. / Tu, Y.H. / Tsai, T.Y. / Maestre-Reyna, M. / Liu, M.S. / Wu, W.J. / Huang, J.Y. / Chi, H.W. / Chang, W.H. / Chiou, C.F. / Wang, A.H. / Lee, J. / Tsai, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6is7.cif.gz | 684.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6is7.ent.gz | 565.1 KB | Display | PDB format |
PDBx/mmJSON format | 6is7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/6is7 ftp://data.pdbj.org/pub/pdb/validation_reports/is/6is7 | HTTPS FTP |
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-Related structure data
Related structure data | 6isfC 6isgC 6ishC 6isiC 4k8xS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 90939.820 Da / Num. of mol.: 2 / Mutation: D141A, E143A, A485L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus sp. 9oN-7 (archaea) / Strain: 9oN-7 / Gene: pol, polA Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q56366, DNA-directed DNA polymerase #2: DNA chain | Mass: 4569.973 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 5541.591 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-CA / #5: 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: 3.15 Å3/Da / Density % sol: 60.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium Acetate pH4.6, MPD, Glycerol, CaCl2 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.29 Å / Num. obs: 63508 / % possible obs: 99.41 % / Redundancy: 2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.04708 / Net I/σ(I): 1.88 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.335 / Num. unique obs: 6242 / CC1/2: 0.703 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K8X Resolution: 2.8→46.29 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.859 / SU B: 33.444 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R: 0.928 / ESU R Free: 0.372 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.663 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→46.29 Å
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Refine LS restraints |
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