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- PDB-3fow: Plasmodium Purine Nucleoside Phosphorylase V66I-V73I-Y160F Mutant -

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Basic information

Entry
Database: PDB / ID: 3fow
TitlePlasmodium Purine Nucleoside Phosphorylase V66I-V73I-Y160F Mutant
ComponentsUridine phosphorylase, putative
KeywordsTRANSFERASE / PROTEIN-inhibitor COMPLEX / phosphorylase / Glycosyltransferase
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 / 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 ribonucleoside salvage / cytosol
Similarity search - Function
Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IMH / PHOSPHATE ION / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDonaldson, T. / Zhan, C.
CitationJournal: Plos One / Year: 2014
Title: Structural determinants of the 5'-methylthioinosine specificity of Plasmodium purine nucleoside phosphorylase.
Authors: Donaldson, T.M. / Ting, L.M. / Zhan, C. / Shi, W. / Zheng, R. / Almo, S.C. / Kim, K.
History
DepositionJan 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Oct 5, 2022Group: Atomic model / Structure summary / Category: atom_site / chem_comp
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.pdbx_synonyms
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine phosphorylase, putative
B: Uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9418
Polymers61,0282
Non-polymers9126
Water1,38777
1
A: Uridine phosphorylase, putative
B: Uridine phosphorylase, putative
hetero molecules

A: Uridine phosphorylase, putative
B: Uridine phosphorylase, putative
hetero molecules

A: Uridine phosphorylase, putative
B: Uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,82224
Polymers183,0856
Non-polymers2,73718
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area26210 Å2
ΔGint-166 kcal/mol
Surface area46230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.969, 234.969, 234.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Uridine phosphorylase, putative /


Mass: 30514.094 Da / Num. of mol.: 2 / Mutation: V66I,V73I,Y160F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PFE0660c, PNP / Plasmid: ptrchis 2 topo / Production host: Escherichia coli (E. coli) / Strain (production host): TOP 10 / References: UniProt: Q8I3X4, uridine phosphorylase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H / Forodesine


Mass: 266.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N4O4 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.43 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 292.15 K / pH: 7.5
Details: 0.2 M Magnesium chloride, 0.1 M HEPES sodium pH 7.5, 30% v/v 2-Propanol, VAPOR DIFFUSION, SITTING DROP, temperature 292.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 27430 / Redundancy: 13.3 % / Biso Wilson estimate: 59.4 Å2 / Rmerge(I) obs: 0.117
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NW4

1nw4


Resolution: 2.8→35.42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.086 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1376 5 %RANDOM
Rwork0.165 ---
obs0.167 25982 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3559 0 58 77 3694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223673
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9964969
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29224.507142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9961518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022662
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.31571
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.52515
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.5304
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.348
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.94822360
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.71633732
X-RAY DIFFRACTIONr_scbond_it5.54331452
X-RAY DIFFRACTIONr_scangle_it7.92641237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 108 -
Rwork0.255 1859 -
obs--99.85 %

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