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- PDB-2bsx: Crystal structure of the Plasmodium falciparum purine nucleoside ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bsx | ||||||
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Title | Crystal structure of the Plasmodium falciparum purine nucleoside phosphorylase complexed with inosine | ||||||
![]() | PURINE NUCLEOSIDE PHOSPHORYLASE | ||||||
![]() | TRANSFERASE / PURINE NUCLEOSIDE PHOSPHORYLASE / URIDINE PHOSPHORYLASE / PUTATIVE / GLYCOSYLTRANSFERASE | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Schnick, C. / Brzozowski, A.M. / Dodson, E.J. / Murshudov, G.N. / Brannigan, J.A. / Wilkinson, A.J. | ||||||
![]() | ![]() Title: Structures of Plasmodium Falciparum Purine Nucleoside Phosphorylase Complexed with Sulfate and its Natural Substrate Inosine Authors: Schnick, C. / Robien, M.A. / Brzozowski, A.M. / Dodson, E.J. / Murshudov, G.N. / Anderson, L. / Luft, J.R. / Mehlin, C. / Hol, W.G.J. / Brannigan, J.A. / Wilkinson, A.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.4 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 786.2 KB | Display | ![]() |
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Full document | ![]() | 795 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1sq6C ![]() 1lx7S 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: 27962.311 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 3D7 / Plasmid: PET28A / Production host: ![]() ![]() References: UniProt: Q8T9Z7, UniProt: Q8I3X4*PLUS, purine-nucleoside phosphorylase |
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#2: Chemical | ChemComp-NOS / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES 246-253 INSERTION FOR CLONING PURPOSE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.6 % |
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Crystal grow | pH: 7.5 Details: 10 % PEG 8000, 0.1 M HEPES PH 7.5, 30 % HEXANETRIOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 12, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9168 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 27984 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5 / % possible all: 80 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LX7 Resolution: 2→18.9 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.852 / SU B: 8.454 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 215-220 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2→18.9 Å
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Refine LS restraints |
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