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

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Basic information

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


S-methyl-5'-thioinosine phosphorylase / uridine catabolic process / 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
PHOSPHATE ION / Quinine / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsChen, D. / Nordlund, P.
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 8, 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

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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)27,5005
Polymers26,8911
Non-polymers6094
Water3,819212
1
A: Purine nucleoside phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)165,00330
Polymers161,3476
Non-polymers3,65624
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Buried area25640 Å2
ΔGint-218 kcal/mol
Surface area45500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.123, 95.123, 47.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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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-QI9 / Quinine / (3alpha,8alpha,9R)-6'-methoxycinchonan-9-ol


Mass: 324.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate tribasic pH 5.6, 1.0M ammonium phosphate monobasic

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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: 1.66→82.38 Å / Num. obs: 29272 / % possible obs: 99.3 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.017 / Rrim(I) all: 0.057 / Net I/σ(I): 27.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.66-1.699.70.213110.9870.0650.21189.3
9.08-47.568.20.0361990.9980.0140.03994.5

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Processing

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

1sq6


Resolution: 1.66→82.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.746 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 1488 5.1 %RANDOM
Rwork0.1635 ---
obs0.1653 27770 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.49 Å2 / Biso mean: 18.522 Å2 / Biso min: 6.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.97 Å2
Refinement stepCycle: final / Resolution: 1.66→82.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1853 0 39 212 2104
Biso mean--17.88 29.38 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191990
X-RAY DIFFRACTIONr_bond_other_d0.0020.021884
X-RAY DIFFRACTIONr_angle_refined_deg2.1971.9632703
X-RAY DIFFRACTIONr_angle_other_deg1.1252.9754376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5215253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66424.56881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8171510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022215
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02386
LS refinement shellResolution: 1.658→1.701 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 102 -
Rwork0.221 1925 -
all-2027 -
obs--94.02 %

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