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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 / transferase / nucleoside phosphorylase
Function / homologyNucleoside phosphorylase domain / Nucleoside phosphorylase superfamily / Phosphorylase superfamily / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / nucleoside metabolic process / Purine nucleoside phosphorylase
Function and homology information
Specimen sourcePlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.3 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 9, 2018 / Release: Jan 16, 2019

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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
Polyers26,8911
Non-polymers4732
Water1,47782
1
A: Purine nucleoside phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,18718
Polyers161,3476
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 area (Å2)21990
ΔGint (kcal/M)-124
Surface area (Å2)46220
MethodPISA
Unit cell
γ
α
β
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-MH 3 2

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Components

#1: Protein/peptide Purine nucleoside phosphorylase /


Mass: 26891.156 Da / Num. of mol.: 1
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 / Formula: PO4 / Phosphate
#3: Chemical ChemComp-YMZ / Mefloquine


Mass: 378.312 Da / Num. of mol.: 1 / Formula: C17H16F6N2O / Mefloquine
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Formula: H2O / Water

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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 / Density percent sol: 44.91 %
Crystal growTemp: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Collection date: Jul 21, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.3 Å / D resolution low: 25.94 Å / Number obs: 10842 / CC half: 0.998 / Rmerge I obs: 0.049 / Rpim I all: 0.023 / Rrim I all: 0.054 / NetI over sigmaI: 21.6 / Number measured all: 59291 / Redundancy: 5.5 % / Scaling rejects: 330 / Percent possible obs: 99.6
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber measured allNumber unique obsCC halfRpim I allRrim I allNetI over sigmaI obsRedundancyPercent possible all
0.0902.3002.380594910650.9970.0420.10010.5005.600100.000
0.0258.91025.9406921740.9980.0140.02929.5004.00083.100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SQ6
Correlation coeff Fo to Fc: 0.95 / Correlation coeff Fo to Fc free: 0.914
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Overall SU B: 7.093 / Overall SU ML: 0.172 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R: 0.349 / Overall ESU R Free: 0.247
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å
Displacement parametersB iso max: 97.26 Å2 / B iso mean: 27.76 Å2 / B iso min: 6.81 Å2 / Aniso B11: -2.3 Å2 / Aniso B12: -1.15 Å2 / Aniso B13: 0 Å2 / Aniso B22: -2.3 Å2 / Aniso B23: 0 Å2 / Aniso B33: 7.46 Å2
Least-squares processR factor R free: 0.2459 / R factor R work: 0.1793 / R factor obs: 0.1827 / Highest resolution: 2.3 Å / Lowest resolution: 25.94 Å / Number reflection R free: 534 / Number reflection obs: 10274 / Percent reflection R free: 4.9 / Percent reflection obs: 99.07
Refine hist #finalHighest resolution: 2.3 Å / Lowest resolution: 25.94 Å / B iso mean ligand: 66.67 / B iso mean solvent: 28.4 / Number residues total: 231
Number of atoms included #finalProtein: 1754 / Nucleic acid: 0 / Ligand: 31 / Solvent: 82 / Total: 1867
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191825
X-RAY DIFFRACTIONr_bond_other_d0.0020.0201737
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9942473
X-RAY DIFFRACTIONr_angle_other_deg1.0383.0004032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5795.000231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.87524.58372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315.000319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.56315.0009
X-RAY DIFFRACTIONr_chiral_restr0.1090.200285
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0202001
X-RAY DIFFRACTIONr_gen_planes_other0.0020.020341
Refine LS shellHighest resolution: 2.3 Å / R factor R free: 0.321 / R factor R free error: 0 / R factor R work: 0.231 / Lowest resolution: 2.36 Å / Number reflection R free: 37 / Number reflection R work: 739 / Number reflection all: 776 / Total number of bins used: 20 / Percent reflection obs: 97.86

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