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- PDB-6ish: Structure of 9N-I DNA polymerase incorporation with 3'-AL in the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ish | ||||||
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Title | Structure of 9N-I DNA polymerase incorporation with 3'-AL in the active site | ||||||
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![]() | TRANSFERASE/DNA / DNA polymerase / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() nucleotide-excision repair, DNA gap filling / 3'-5'-DNA exonuclease activity / DNA replication proofreading / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Linwu, S.W. / Maestre-Reyna, M. / Tsai, M.D. / Tu, Y.H. / Chang, W.H. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.9 KB | Display | ![]() |
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PDB format | ![]() | 265.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6is7C ![]() 6isfC ![]() 6isgC ![]() 6isiC ![]() 4k8xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 90939.820 Da / Num. of mol.: 1 / Mutation: D141A, E143A, A485L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: Q56366, DNA-directed DNA polymerase |
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-DNA chain , 2 types, 2 molecules CD
#2: DNA chain | Mass: 4256.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 5212.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 26 molecules ![](data/chem/img/PPV.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/B9X.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/B9X.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PPV / | ||||
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#5: Chemical | #6: Chemical | ChemComp-B9X / [( | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.77 % |
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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: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→48.99 Å / Num. obs: 21653 / % possible obs: 96.1 % / Redundancy: 1.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.04456 / Net I/σ(I): 6.73 |
Reflection shell | Resolution: 3.301→3.419 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 2203 / CC1/2: 0.654 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K8X Resolution: 3.3→48.99 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.882 / SU B: 57.849 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.522 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.998 Å2
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Refinement step | Cycle: 1 / Resolution: 3.3→48.99 Å
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Refine LS restraints |
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