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- PDB-7omg: Crystal structure of KOD DNA Polymerase in a ternary complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7omg | ||||||
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Title | Crystal structure of KOD DNA Polymerase in a ternary complex with an Uracil containing template | ||||||
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![]() | REPLICATION / ternary complex / DNA polymerase / uracil | ||||||
Function / homology | ![]() intein-mediated protein splicing / intron homing / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-templated DNA replication / endonuclease activity / DNA-directed DNA polymerase ...intein-mediated protein splicing / intron homing / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-templated DNA replication / endonuclease activity / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Betz, K. / Kropp, H.M. / Diederichs, K. / Marx, A. | ||||||
![]() | ![]() Title: Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase. Authors: Kropp, H.M. / Ludmann, S. / Diederichs, K. / Betz, K. / Marx, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.5 KB | Display | ![]() |
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PDB format | ![]() | 292.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 890.8 KB | Display | ![]() |
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Full document | ![]() | 902.6 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7om3C ![]() 7ombC ![]() 5omfS 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: 90060.461 Da / Num. of mol.: 1 / Mutation: D141A,E143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: pol, TK0001 / Production host: ![]() ![]() |
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-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 6431.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3601.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 7 types, 97 molecules ![](data/chem/img/DTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DTP / | ||||||||||
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#5: Chemical | #6: Chemical | ChemComp-MN / | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-CL / | #10: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.55 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: Morpheus A3: 0.06MDivalents (0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate) 0.1M Buffer System 1 (1 M MES/Imidazol pH 6.5) 30% v/vPrecipitant Mix 3 (40% v/v Glycerol; 20% w/v PEG 4000) PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000009 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→49.026 Å / Num. obs: 66516 / % possible obs: 99.2 % / Redundancy: 9.8 % / Biso Wilson estimate: 53.96 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.142 / Net I/σ(I): 11.49 |
Reflection shell | Resolution: 2.1→2.23 Å / Mean I/σ(I) obs: 0.39 / Num. unique obs: 10239 / CC1/2: 0.157 / Rrim(I) all: 0.4266 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OMF Resolution: 2.1→46.25 Å / SU ML: 0.494 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 35.0045 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→46.25 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 | Refine-ID: X-RAY DIFFRACTION
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