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- PDB-6aqu: Crystal Structure of Plasmodium falciparum purine nucleoside phos... -

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Basic information

Entry
Database: PDB / ID: 6aqu
TitleCrystal Structure of Plasmodium falciparum purine nucleoside phosphorylase: The M183L mutant
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Plasmodium falciparum / Purine nucleoside phosphorylase (PNP) / PNP mutation / drug resistant PNP.
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
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: 2.6 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 inPlasmodium falciparum.
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 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3195
Polymers54,0352
Non-polymers2853
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-33 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.500, 132.500, 115.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 245 / Label seq-ID: 5 - 247

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Purine nucleoside phosphorylase


Mass: 27017.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: na
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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.3 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM Sodium Acetate, 20 %(w/v) PEG 3350

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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-225 / Detector: CCD / Date: Jul 12, 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: 2.6→93.69 Å / Num. obs: 16166 / % possible obs: 99.9 % / Redundancy: 16 % / CC1/2: 0.99 / Net I/σ(I): 18
Reflection shellResolution: 2.6→2.72 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1935 / CC1/2: 0.58 / % 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: 3PHC

3phc


Resolution: 2.6→93.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.717 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R: 0.828 / ESU R Free: 0.354 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28723 791 4.9 %RANDOM
Rwork0.24183 ---
obs0.24409 15361 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.173 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: 1 / Resolution: 2.6→93.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 15 12 3342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193369
X-RAY DIFFRACTIONr_bond_other_d0.0020.023226
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9794551
X-RAY DIFFRACTIONr_angle_other_deg0.96837473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48524.846130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.94415591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4551515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02617
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_it5.3737.8151761
X-RAY DIFFRACTIONr_mcbond_other5.3747.8121760
X-RAY DIFFRACTIONr_mcangle_it8.28911.6922189
X-RAY DIFFRACTIONr_mcangle_other8.28911.6952190
X-RAY DIFFRACTIONr_scbond_it5.1918.4331608
X-RAY DIFFRACTIONr_scbond_other5.1168.4291597
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.12312.4082345
X-RAY DIFFRACTIONr_long_range_B_refined11.53493.6093620
X-RAY DIFFRACTIONr_long_range_B_other11.53593.6323620
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12790 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 64 -
Rwork0.356 1105 -
obs--100 %

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