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- PDB-7sxl: Plasmodium falciparum apicoplast DNA polymerase (exo-minus) witho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sxl | |||||||||
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Title | Plasmodium falciparum apicoplast DNA polymerase (exo-minus) without affinity tag | |||||||||
![]() | Plastid replication-repair enzyme | |||||||||
![]() | REPLICATION / Transferase / DNA polymerase / exonulease / apicoplast | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Nieto, N. / Chheda, P. / Kerns, R. / Nelson, S. / Honzatko, R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Promising antimalarials targeting apicoplast DNA polymerase from Plasmodium falciparum. Authors: Chheda, P.R. / Nieto, N. / Kaur, S. / Beck, J.M. / Beck, J.R. / Honzatko, R. / Kerns, R.J. / 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 | ![]() | 577.4 KB | Display | ![]() |
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PDB format | ![]() | 389.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.7 KB | Display | ![]() |
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Full document | ![]() | 489.4 KB | Display | |
Data in XML | ![]() | 43.4 KB | Display | |
Data in CIF | ![]() | 61.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sxqC ![]() 5dkuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 74002.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: isolate 3D7 / Gene: PF3D7_1411400 Production host: ![]() ![]() References: UniProt: Q8ILY1, DNA-directed DNA polymerase |
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-Non-polymers , 6 types, 391 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.82 % / Description: Hexagonal bipyramidal |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Equal parts protein and precipitant solutions. Protein solution: 20 mg/ml protein, 20 mM Tris, pH 8.0, 500 mM NaCl, 10% glycerol and 5 mM imidazole. Precipitant solution: PEG 1000 30% (v/v), ...Details: Equal parts protein and precipitant solutions. Protein solution: 20 mg/ml protein, 20 mM Tris, pH 8.0, 500 mM NaCl, 10% glycerol and 5 mM imidazole. Precipitant solution: PEG 1000 30% (v/v), 100 sodium citrate tribasic dihydrate, pH 5.5, 400 mM NaCl. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→19.91 Å / Num. obs: 54200 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 61.4 Å2 / CC1/2: 0.99 / Net I/σ(I): 0.8 |
Reflection shell | Resolution: 2.7→2.75 Å / Num. unique obs: 2312 / CC1/2: 0.539 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DKU Resolution: 2.7→19.91 Å / SU ML: 0.3206 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.578 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: 72.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→19.91 Å
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Refine LS restraints |
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LS refinement shell |
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