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Yorodumi- PDB-7sxl: Plasmodium falciparum apicoplast DNA polymerase (exo-minus) witho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sxl | |||||||||
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Title | Plasmodium falciparum apicoplast DNA polymerase (exo-minus) without affinity tag | |||||||||
Components | Plastid replication-repair enzyme | |||||||||
Keywords | REPLICATION / Transferase / DNA polymerase / exonulease / apicoplast | |||||||||
Function / homology | Function and homology information 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 | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Nieto, N. / Chheda, P. / Kerns, R. / Nelson, S. / Honzatko, R. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sxl.cif.gz | 577.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sxl.ent.gz | 389.2 KB | Display | PDB format |
PDBx/mmJSON format | 7sxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sxl_validation.pdf.gz | 479.7 KB | Display | wwPDB validaton report |
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Full document | 7sxl_full_validation.pdf.gz | 489.4 KB | Display | |
Data in XML | 7sxl_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 7sxl_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/7sxl ftp://data.pdbj.org/pub/pdb/validation_reports/sx/7sxl | HTTPS FTP |
-Related structure data
Related structure data | 7sxqC 5dkuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF3D7_1411400 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8ILY1, DNA-directed DNA polymerase |
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-Non-polymers , 6 types, 391 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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