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- PDB-7omb: 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: 7omb | ||||||
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Title | Crystal structure of KOD DNA Polymerase in a ternary complex with a p/t duplex containing an extended 5' single stranded template overhang | ||||||
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![]() | REPLICATION / ternary complex / DNA polymerase | ||||||
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 | ![]() | 621.9 KB | Display | ![]() |
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PDB format | ![]() | 425.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 887.1 KB | Display | ![]() |
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Full document | ![]() | 896 KB | Display | |
Data in XML | ![]() | 32 KB | Display | |
Data in CIF | ![]() | 46.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7om3C ![]() 7omgC ![]() 5omfS C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 90060.461 Da / Num. of mol.: 1 / Mutation: Asp141Ala Glu143Ala 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: 6470.169 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 , 5 types, 289 molecules ![](data/chem/img/DTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DTP / | ||||||
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#5: Chemical | #6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-EDO / #8: 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: 2.82 Å3/Da / Density % sol: 56.45 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus E7: 0.12 M ethylene glycols (0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol), 0.1 M sodium HEPES/MOPS pH 7.5, 50 % (v/v) ...Details: Morpheus E7: 0.12 M ethylene glycols (0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol), 0.1 M sodium HEPES/MOPS pH 7.5, 50 % (v/v) of a mixture of glycerol (40 % v/v) and PEG 4000 (20 % w/v) |
-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: Nov 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999977 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→49.051 Å / Num. obs: 145908 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.18 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.162 / Net I/σ(I): 6.32 |
Reflection shell | Resolution: 2.01→2.13 Å / Mean I/σ(I) obs: 0.45 / Num. unique obs: 22740 / CC1/2: 0.178 / Rrim(I) all: 0.217 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OMF Resolution: 2.01→46.28 Å / SU ML: 0.3408 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8429 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: 50.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→46.28 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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