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- PDB-8w7h: Purine Nucleoside Phosphorylase in complex with MMV000848 -

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Basic information

Entry
Database: PDB / ID: 8w7h
TitlePurine Nucleoside Phosphorylase in complex with MMV000848
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE/INHIBITOR / Protein binding / TRANSFERASE-inhibitor complex
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 / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Chem-XUH / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChung, Z. / Lin, J.Q. / Lescar, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Identification and structural validation of purine nucleoside phosphorylase from Plasmodium falciparum as a target of MMV000848.
Authors: Chung, Z. / Lin, J. / Wirjanata, G. / Dziekan, J.M. / El Sahili, A. / Preiser, P.R. / Bozdech, Z. / Lescar, J.
History
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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)28,3036
Polymers27,7911
Non-polymers5115
Water3,063170
1
A: Purine nucleoside phosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)169,81536
Polymers166,7476
Non-polymers3,06930
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
4
A: Purine nucleoside phosphorylase
hetero molecules


  • crystal asymmetric unit, crystal frame
  • 28.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)28,3036
Polymers27,7911
Non-polymers5115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
Unit cell
Length a, b, c (Å)95.610, 95.610, 138.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
SymmetryPoint symmetry: (Schoenflies symbol: D3 (2x3 fold dihedral))
Components on special symmetry positions
IDModelComponents
11A-303-

NA

21A-304-

NA

31A-420-

HOH

41A-476-

HOH

51A-483-

HOH

61A-556-

HOH

71A-568-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Purine nucleoside phosphorylase


Mass: 27791.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PNP / Plasmid: pNIC-CH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8I3X4

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-XUH / (2R)-1-(9H-carbazol-9-yl)-3-(cyclopentylamino)propan-2-ol


Mass: 308.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% (w/v) PEG 1000, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Nitrogen gas / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→33.17 Å / Num. obs: 20977 / % possible obs: 99.79 % / Redundancy: 20.3 % / Biso Wilson estimate: 27.17 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0743 / Rpim(I) all: 0.01689 / Rrim(I) all: 0.07623 / Net I/σ(I): 30.42
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 20.7 % / Rmerge(I) obs: 0.9243 / Mean I/σ(I) obs: 3.73 / Num. unique obs: 2065 / CC1/2: 0.953 / CC star: 0.988 / Rpim(I) all: 0.2069 / Rrim(I) all: 0.9475 / % possible all: 99.32

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→33.17 Å / SU ML: 0.2082 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.3595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1767 1048 5.02 %
Rwork0.1726 38164 -
obs-20951 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.11 Å2
Refinement stepCycle: LAST / Resolution: 1.85→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 34 170 1971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891872
X-RAY DIFFRACTIONf_angle_d1.15042535
X-RAY DIFFRACTIONf_chiral_restr0.0695291
X-RAY DIFFRACTIONf_plane_restr0.0082322
X-RAY DIFFRACTIONf_dihedral_angle_d16.3315697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.34541400.32992701X-RAY DIFFRACTION97.56
1.9-1.950.33371450.3052723X-RAY DIFFRACTION99.58
1.95-20.29811440.24712709X-RAY DIFFRACTION99.93
2-2.070.24351450.22752733X-RAY DIFFRACTION99.86
2.07-2.140.22221460.20912689X-RAY DIFFRACTION99.82
2.14-2.230.20951460.20492743X-RAY DIFFRACTION99.83
2.23-2.330.25011450.2082727X-RAY DIFFRACTION99.27
2.33-2.450.20561440.17662715X-RAY DIFFRACTION99.79
2.45-2.610.17461430.17872732X-RAY DIFFRACTION100
2.61-2.810.19041420.16322745X-RAY DIFFRACTION100
2.81-3.090.16751440.16912726X-RAY DIFFRACTION100
3.09-3.540.15391400.15562748X-RAY DIFFRACTION100
3.54-4.450.14851470.13022734X-RAY DIFFRACTION99.93
4.46-33.170.11671440.15222739X-RAY DIFFRACTION99.9

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