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Yorodumi- PDB-5znc: Plasmodium falciparum purine nucleoside phosphorylase in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5znc | ||||||
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Title | Plasmodium falciparum purine nucleoside phosphorylase in complex with quinine | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE / nucleoside phosphorylase | ||||||
Function / homology | Function and homology information S-methyl-5'-thioinosine phosphorylase / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Chen, D. / Nordlund, P. | ||||||
Citation | Journal: Sci Transl Med / Year: 2019 Title: Identifying purine nucleoside phosphorylase as the target of quinine using cellular thermal shift assay. Authors: Dziekan, J.M. / Yu, H. / Chen, D. / Dai, L. / Wirjanata, G. / Larsson, A. / Prabhu, N. / Sobota, R.M. / Bozdech, Z. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5znc.cif.gz | 68.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5znc.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 5znc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/5znc ftp://data.pdbj.org/pub/pdb/validation_reports/zn/5znc | HTTPS FTP |
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-Related structure data
Related structure data | 5zniC 1sq6S 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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-Components
#1: Protein | Mass: 26891.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PNP / Production host: Escherichia coli (E. coli) References: UniProt: Q8T9Z7, purine-nucleoside phosphorylase | ||
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#2: Chemical | ChemComp-QI9 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium citrate tribasic pH 5.6, 1.0M ammonium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 21, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.66→82.38 Å / Num. obs: 29272 / % possible obs: 99.3 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Net I/σ(I): 27.7 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SQ6 Resolution: 1.66→82.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.746 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 70.49 Å2 / Biso mean: 18.522 Å2 / Biso min: 6.75 Å2
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Refinement step | Cycle: final / Resolution: 1.66→82.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.658→1.701 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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