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- PDB-6aqs: Crystal structure of Plasmodium falciparum purine nucleoside phos... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6aqs | ||||||
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Title | Crystal structure of Plasmodium falciparum purine nucleoside phosphorylase (V181D) mutant complexed with DADMe-ImmG and phosphate | ||||||
![]() | Purine nucleoside phosphorylase | ||||||
![]() | TRANSFERASE / Plasmodium falciparum / purine nucleoside phosphorylase (PNP) / Phosphorylase / PNP mutant / DADMe-ImmG | ||||||
Function / homology | ![]() Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine catabolic process / guanosine phosphorylase activity / uridine phosphorylase activity / purine-nucleoside phosphorylase ...Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / S-methyl-5-thioadenosine phosphorylase activity / inosine catabolic process / uridine catabolic process / guanosine phosphorylase activity / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine nucleoside catabolic process / purine ribonucleoside salvage / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harijan, R.K. / Ducati, R.G. / Namanja-Magliano, H.A. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
![]() | ![]() Title: Genetic resistance to purine nucleoside phosphorylase inhibition in Authors: Ducati, R.G. / Namanja-Magliano, H.A. / Harijan, R.K. / Fajardo, J.E. / Fiser, A. / Daily, J.P. / Schramm, V.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.6 KB | Display | ![]() |
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PDB format | ![]() | 44.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 829.7 KB | Display | ![]() |
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Full document | ![]() | 829.9 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6aquC ![]() 3phcS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 26994.191 Da / Num. of mol.: 1 / Mutation: V181D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PNP / Production host: ![]() ![]() References: UniProt: Q8T9Z7, UniProt: Q8I3X4*PLUS, purine-nucleoside phosphorylase | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-IM5 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.72 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 100 mM tri-sodium citrate, pH 5.6, 200 mM ammonium sulfate, 15% w/v PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225HE / Detector: CCD / Date: Aug 9, 2017 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→45.19 Å / Num. obs: 33133 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.99 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1621 / CC1/2: 0.75 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3PHC Resolution: 1.57→45.19 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.066 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.783 Å2
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Refinement step | Cycle: LAST / Resolution: 1.57→45.19 Å
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Refine LS restraints |
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