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- PDB-1nw4: Crystal Structure of Plasmodium falciparum Purine Nucleoside Phos... -

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Basic information

Entry
Database: PDB / ID: 1nw4
TitleCrystal Structure of Plasmodium falciparum Purine Nucleoside Phosphorylase in complex with ImmH and Sulfate
Componentsuridine phosphorylase, putative
KeywordsTRANSFERASE / Transition State Complex
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
Chem-IMH / ISOPROPYL ALCOHOL / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShi, W. / Ting, L.M. / Kicska, G.A. / Lewandowicz, A. / Tyler, P.C. / Evans, G.B. / Furneaux, R.H. / Kim, K. / Almo, S.C. / Schramm, V.L.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Plasmodium falciparum Purine Nucleoside Phosphorylase: CRYSTAL STRUCTURES, IMMUCILLIN INHIBITORS, AND DUAL CATALYTIC FUNCTION.
Authors: Shi, W. / Ting, L.M. / Kicska, G.A. / Lewandowicz, A. / Tyler, P.C. / Evans, G.B. / Furneaux, R.H. / Kim, K. / Almo, S.C. / Schramm, V.L.
History
DepositionFeb 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 2.0Oct 5, 2022Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Experimental preparation / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / exptl_crystal / struct_ref_seq_dif / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uridine phosphorylase, putative
B: uridine phosphorylase, putative
C: uridine phosphorylase, putative
D: uridine phosphorylase, putative
E: uridine phosphorylase, putative
F: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,33646
Polymers183,0126
Non-polymers4,32440
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: uridine phosphorylase, putative
E: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,35314
Polymers61,0042
Non-polymers1,34912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-89 kcal/mol
Surface area20470 Å2
MethodPISA
3
A: uridine phosphorylase, putative
F: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,66618
Polymers61,0042
Non-polymers1,66216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-114 kcal/mol
Surface area20510 Å2
MethodPISA
4
B: uridine phosphorylase, putative
C: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31714
Polymers61,0042
Non-polymers1,31312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-80 kcal/mol
Surface area20530 Å2
MethodPISA
5
E: uridine phosphorylase, putative
F: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,51016
Polymers61,0042
Non-polymers1,50514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-98 kcal/mol
Surface area18550 Å2
MethodPISA
6
C: uridine phosphorylase, putative
D: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,19712
Polymers61,0042
Non-polymers1,19310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-70 kcal/mol
Surface area18760 Å2
MethodPISA
7
A: uridine phosphorylase, putative
B: uridine phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,63018
Polymers61,0042
Non-polymers1,62616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-97 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.554, 92.285, 239.640
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a hexamer in the asymmetric unit.

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Components

#1: Protein
uridine phosphorylase, putative


Mass: 30502.039 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: pTrcHis2-TOPO / Production host: Escherichia coli (E. coli)
References: UniProt: Q8I3X4, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMH / 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL / Forodesine / Immucillin H


Mass: 266.253 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H14N4O4 / Comment: inhibitor*YM
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.61 Å3/Da / Density % sol: 57.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Ammonium Sulfate, Isopropanol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1dropwith ImmH
23 mMsodium phosphate1drop
31.6 Mammonium sulfate1reservoir
43 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 30, 2002
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 81643 / Num. obs: 81643 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 11.6
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 6610 / Rsym value: 0.249 / % possible all: 68.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A69

1a69


Resolution: 2.2→20 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3874 5 %RANDOM
Rwork0.207 ---
obs0.209 76950 78.5 %-
all-79193 --
Solvent computationSolvent model: Flat model / Bsol: 46.2852 Å2 / ksol: 0.387935 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1--7.65 Å20 Å20 Å2
2--10.3 Å20 Å2
3----2.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11166 0 269 248 11683
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 504 5.2 %
Rwork0.275 9240 -
obs-9744 60.3 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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