+Open data
-Basic information
Entry | Database: PDB / ID: 8w7h | ||||||
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Title | Purine Nucleoside Phosphorylase in complex with MMV000848 | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE/INHIBITOR / Protein binding / TRANSFERASE-inhibitor complex | ||||||
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 phosphorylase activity / purine ribonucleoside salvage / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Chung, Z. / Lin, J.Q. / Lescar, J. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Identification and structural validation of purine nucleoside phosphorylase from Plasmodium falciparum as a target of MMV000848. Authors: Chung, Z. / Lin, J. / Wirjanata, G. / Dziekan, J.M. / El Sahili, A. / Preiser, P.R. / Bozdech, Z. / Lescar, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w7h.cif.gz | 121 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w7h.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 8w7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/8w7h ftp://data.pdbj.org/pub/pdb/validation_reports/w7/8w7h | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: D3 (2x3 fold dihedral)) | ||||||||||||||||||||||||
Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 27791.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PNP / Plasmid: pNIC-CH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8I3X4 |
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-Non-polymers , 5 types, 175 molecules
#2: Chemical | ChemComp-XUH / ( | ||||
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#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% (w/v) PEG 1000, 10% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: Nitrogen gas / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→33.17 Å / Num. obs: 20977 / % possible obs: 99.79 % / Redundancy: 20.3 % / Biso Wilson estimate: 27.17 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0743 / Rpim(I) all: 0.01689 / Rrim(I) all: 0.07623 / Net I/σ(I): 30.42 |
Reflection shell | Resolution: 1.85→1.916 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.9243 / Mean I/σ(I) obs: 3.73 / Num. unique obs: 2065 / CC1/2: 0.953 / CC star: 0.988 / Rpim(I) all: 0.2069 / Rrim(I) all: 0.9475 / % possible all: 99.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.17 Å / SU ML: 0.2082 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3595 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: 39.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→33.17 Å
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Refine LS restraints |
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LS refinement shell |
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