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- PDB-3iex: Schistosoma Purine nucleoside phosphorylase in complex with guanosine -

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Basic information

Entry
Database: PDB / ID: 3iex
TitleSchistosoma Purine nucleoside phosphorylase in complex with guanosine
ComponentsPurine-nucleoside phosphorylase
KeywordsTRANSFERASE / Purine nucleoside phosphorylase / Glycosyltransferase
Function / homology
Function and homology information


nucleoside metabolic process / guanosine phosphorylase activity / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Purine nucleoside phosphorylase I, inosine/guanosine-specific / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCastilho, M.S. / Pereira, H.M. / Oliva, G. / Andricopulo, A.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Structural basis for selective inhibition of purine nucleoside phosphorylase from Schistosoma mansoni: kinetic and structural studies
Authors: Castilho, M.S. / Postigo, M.P. / Pereira, H.M. / Oliva, G. / Andricopulo, A.D.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,72212
Polymers93,5923
Non-polymers1,1309
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-53 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.212, 118.195, 129.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Purine-nucleoside phosphorylase


Mass: 31197.254 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: SmPNP / Plasmid: pMAL-c2g / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q9BMI9, purine-nucleoside phosphorylase

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Non-polymers , 5 types, 571 molecules

#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 1500, 20% GLYCEROL, 32mM SODIUM ACETATE, pH 4.9-5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 4.9-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 44386 / % possible obs: 94.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.049

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TD1

1td1


Resolution: 2.05→43.628 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.844 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 2236 5.04 %
Rwork0.1752 42091 -
obs0.1782 44327 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.849 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 135 Å2 / Biso mean: 37.868 Å2 / Biso min: 15.19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 70 562 6844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066383
X-RAY DIFFRACTIONf_angle_d1.0448646
X-RAY DIFFRACTIONf_chiral_restr0.061020
X-RAY DIFFRACTIONf_plane_restr0.0041099
X-RAY DIFFRACTIONf_dihedral_angle_d17.692323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.0950.2831020.2232327242982
2.095-2.1430.2481310.1982345247687
2.143-2.1970.2781410.192439258087
2.197-2.2560.2491290.2022444257390
2.256-2.3230.2971520.1912518267091
2.323-2.3980.2361430.1812544268792
2.398-2.4830.2691280.1832626275495
2.483-2.5830.271320.1792645277794
2.583-2.70.2171100.1692663277395
2.7-2.8430.221280.1662701282996
2.843-3.0210.2291440.1642731287597
3.021-3.2540.2061800.1622705288598
3.254-3.5810.231500.1552769291999
3.581-4.0990.1821500.1422790294098
4.099-5.1630.2031520.142866301899
5.163-43.6380.271640.2082978314299

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