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- PDB-5zni: Plasmodium falciparum purine nucleoside phosphorylase in complex ... -

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Basic information

Entry
Database: PDB / ID: 5zni
TitlePlasmodium falciparum purine nucleoside phosphorylase in complex with mefloquine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / nucleoside phosphorylase
Function / homology
Function and homology information


S-methyl-5'-thioinosine phosphorylase / 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
PHOSPHATE ION / Mefloquine / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, D. / Nordlund, P. / Dziekan, J.M.
CitationJournal: 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
DepositionApr 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)27,3643
Polymers26,8911
Non-polymers4732
Water1,47782
1
A: Purine nucleoside phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,18718
Polymers161,3476
Non-polymers2,84012
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 area21990 Å2
ΔGint-124 kcal/mol
Surface area46220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.591, 95.591, 136.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Purine nucleoside phosphorylase


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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-YMZ / (11R,12S)- Mefloquine


Mass: 378.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H16F6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→25.94 Å / Num. obs: 10842 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.023 / Rrim(I) all: 0.054 / Net I/σ(I): 21.6 / Num. measured all: 59291 / Scaling rejects: 330
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.385.60.09594910650.9970.0420.110.5100
8.91-25.9440.0256921740.9980.0140.02929.583.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SQ6

1sq6


Resolution: 2.3→25.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.914 / SU B: 7.093 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.349 / ESU R Free: 0.247
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 534 4.9 %RANDOM
Rwork0.1793 ---
obs0.1827 10274 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.26 Å2 / Biso mean: 27.76 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å2-1.15 Å20 Å2
2---2.3 Å20 Å2
3---7.46 Å2
Refinement stepCycle: final / Resolution: 2.3→25.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 31 82 1867
Biso mean--66.67 28.4 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191825
X-RAY DIFFRACTIONr_bond_other_d0.0020.021737
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9942473
X-RAY DIFFRACTIONr_angle_other_deg1.03834032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.87524.58372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.563159
X-RAY DIFFRACTIONr_chiral_restr0.1090.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022001
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02341
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 37 -
Rwork0.231 739 -
all-776 -
obs--97.86 %

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