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Yorodumi- PDB-6aqu: Crystal Structure of Plasmodium falciparum purine nucleoside phos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aqu | ||||||
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Title | Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase: The M183L mutant | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / Plasmodium falciparum / Purine nucleoside phosphorylase (PNP) / PNP mutation / drug resistant PNP. | ||||||
Function / homology | Function and homology information 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 / uridine phosphorylase activity / guanosine 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 / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine nucleoside catabolic process / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Harijan, R.K. / Ducati, R.G. / Namanja-Magliano, H.A. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Genetic resistance to purine nucleoside phosphorylase inhibition inPlasmodium falciparum. 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aqu.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aqu.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 6aqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/6aqu ftp://data.pdbj.org/pub/pdb/validation_reports/aq/6aqu | HTTPS FTP |
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-Related structure data
Related structure data | 6aqsC 3phcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 245 / Label seq-ID: 5 - 247
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-Components
#1: Protein | Mass: 27017.252 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: na Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PNP / Production host: Escherichia coli (E. coli) References: UniProt: Q8T9Z7, UniProt: Q8I3X4*PLUS, purine-nucleoside phosphorylase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 47.7 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM Sodium Acetate, 20 %(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 12, 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: 2.6→93.69 Å / Num. obs: 16166 / % possible obs: 99.9 % / Redundancy: 16 % / CC1/2: 0.99 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1935 / CC1/2: 0.58 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PHC Resolution: 2.6→93.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.717 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R: 0.828 / ESU R Free: 0.354 / 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: 79.173 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→93.69 Å
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Refine LS restraints |
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