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Open data
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Basic information
Entry | Database: PDB / ID: 5dkt | ||||||
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Title | N-terminal His tagged apPOL exonuclease mutant | ||||||
![]() | Prex DNA polymerase | ||||||
![]() | TRANSFERASE / DNA polymerase | ||||||
Function / homology | ![]() apicoplast / mitochondrial DNA replication / DNA primase activity / DNA helicase activity / 3'-5' exonuclease activity / single-stranded DNA binding / 5'-3' DNA helicase activity / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Milton, M.E. / Honzatko, R.B. / Choe, J.Y. / Nelson, S.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of the Apicoplast DNA Polymerase from Plasmodium falciparum: The First Look at a Plastidic A-Family DNA Polymerase. Authors: Milton, M.E. / Choe, J.Y. / Honzatko, R.B. / Nelson, S.W. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2015 Title: Crystallization and preliminary X-ray analysis of the Plasmodium falciparum apicoplast DNA polymerase. Authors: Milton, M.E. / Choe, J.Y. / Honzatko, R.B. / Nelson, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.1 KB | Display | ![]() |
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PDB format | ![]() | 195 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.9 KB | Display | ![]() |
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Full document | ![]() | 452.2 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dkuC ![]() 2kfnS 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
#1: Protein | Mass: 76174.250 Da / Num. of mol.: 1 / Fragment: UNP residues 1389-2016 / Mutation: D82N, E84Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: POM1, PF14_0112 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M ammonium sulfate, 0.1 M MES monohydrate pH 6.5, 30%(w/v) PEG monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 19706 / % possible obs: 97.8 % / Observed criterion σ(I): -1 / Redundancy: 4.2 % / Biso Wilson estimate: 47.25 Å2 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.195 / Rrim(I) all: 0.339 / Χ2: 1.07 / Net I/av σ(I): 3.373 / Net I/σ(I): 2.5 / Num. measured all: 82305 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2KFN Resolution: 2.9→47.346 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.3 / Stereochemistry target values: ML
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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 max: 206.99 Å2 / Biso mean: 53.5513 Å2 / Biso min: 0.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.9→47.346 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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