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- PDB-6aqs: Crystal structure of Plasmodium falciparum purine nucleoside phos... -

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Basic information

Entry
Database: PDB / ID: 6aqs
TitleCrystal structure of Plasmodium falciparum purine nucleoside phosphorylase (V181D) mutant complexed with DADMe-ImmG and phosphate
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Plasmodium falciparum / purine nucleoside phosphorylase (PNP) / Phosphorylase / PNP mutant / DADMe-ImmG
Function / homology
Function and homology information


Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / uridine catabolic process / inosine catabolic process / S-methyl-5-thioadenosine phosphorylase activity / uridine phosphorylase activity / guanosine phosphorylase activity / purine-nucleoside phosphorylase ...Pyrimidine salvage / Pyrimidine catabolism / S-methyl-5'-thioinosine phosphorylase / purine nucleotide catabolic process / uridine catabolic process / inosine catabolic process / S-methyl-5-thioadenosine phosphorylase activity / uridine phosphorylase activity / guanosine 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-IM5 / PHOSPHATE ION / Purine nucleoside phosphorylase / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsHarijan, R.K. / Ducati, R.G. / Namanja-Magliano, H.A. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Genetic resistance to purine nucleoside phosphorylase inhibition in
Authors: Ducati, R.G. / Namanja-Magliano, H.A. / Harijan, R.K. / Fajardo, J.E. / Fiser, A. / Daily, J.P. / Schramm, V.L.
History
DepositionAug 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4935
Polymers26,9941
Non-polymers4984
Water2,774154
1
A: Purine nucleoside phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,95630
Polymers161,9656
Non-polymers2,99024
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area22840 Å2
ΔGint-108 kcal/mol
Surface area45560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.110, 95.110, 135.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

21A-448-

HOH

31A-484-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase


Mass: 26994.191 Da / Num. of mol.: 1 / Mutation: V181D
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, UniProt: Q8I3X4*PLUS, purine-nucleoside phosphorylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-IM5 / 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one / DADMe-ImmG


Mass: 279.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N5O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 100 mM tri-sodium citrate, pH 5.6, 200 mM ammonium sulfate, 15% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225HE / Detector: CCD / Date: Aug 9, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.57→45.19 Å / Num. obs: 33133 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.99 / Net I/σ(I): 13.7
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1621 / CC1/2: 0.75 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PHC

3phc


Resolution: 1.57→45.19 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.066 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21474 1633 4.9 %RANDOM
Rwork0.18339 ---
obs0.18486 31499 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.783 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å2-0.71 Å20 Å2
2---1.42 Å20 Å2
3---4.62 Å2
Refinement stepCycle: LAST / Resolution: 1.57→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 33 156 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191807
X-RAY DIFFRACTIONr_bond_other_d0.0020.021735
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9942440
X-RAY DIFFRACTIONr_angle_other_deg0.91434026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6424.64871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.152159
X-RAY DIFFRACTIONr_chiral_restr0.0750.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021974
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3132.205918
X-RAY DIFFRACTIONr_mcbond_other1.3062.201917
X-RAY DIFFRACTIONr_mcangle_it2.2423.2871144
X-RAY DIFFRACTIONr_mcangle_other2.2443.2911145
X-RAY DIFFRACTIONr_scbond_it1.6162.505887
X-RAY DIFFRACTIONr_scbond_other1.6152.505887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7053.6651297
X-RAY DIFFRACTIONr_long_range_B_refined4.47926.891996
X-RAY DIFFRACTIONr_long_range_B_other4.47826.9091997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 136 -
Rwork0.352 2302 -
obs--100 %

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