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- PDB-3faz: Crystal structure of Schistosoma mansoni purine nucleoside phosph... -

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Basic information

Entry
Database: PDB / ID: 3faz
TitleCrystal structure of Schistosoma mansoni purine nucleoside phosphorylase in complex with inosine
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
INOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsPereira, H.M. / Garratt, R.C. / Oliva, G.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme from Schistosoma mansoni.
Authors: Pereira, H.M. / Rezende, M.M. / Castilho, M.S. / Oliva, G. / Garratt, R.C.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Structures for the potential drug target purine nucleoside phosphorylase from Schistosoma mansoni causal agent of schistosomiasis.
Authors: Pereira, H.D. / Franco, G.R. / Cleasby, A. / Garratt, R.C.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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)94,5898
Polymers93,5923
Non-polymers9975
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-56.1 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.785, 118.668, 129.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.01 Å3/Da / Density % sol: 38.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 18-20% PEG 1500, 20% Glycerol, 32mM Sodium acetate, VAPOR DIFFUSION, temperature 277K
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: 1.459 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.9→87.706 Å / Num. obs: 60248 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 9.028
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-24.50.4861.53934686620.48699.8
2-2.124.50.2932.43723882380.29399.8
2.12-2.274.50.2043.43483076930.20499.9
2.27-2.454.50.1415.13298772570.141100
2.45-2.694.70.0997.13143066820.099100
2.69-34.90.0719.62980260710.071100
3-3.4750.05212.62719553940.052100
3.47-4.2550.0415.52301345770.04100
4.25-6.0150.03317.71808936190.03399.9
6.01-87.7064.70.03317967920550.03398.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TD1

1td1


Resolution: 1.9→39.018 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.27 / σ(F): 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.237 2904 5.06 %
Rwork0.181 --
obs0.184 57361 95.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.725 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 106.03 Å2 / Biso mean: 38.63 Å2 / Biso min: 14.63 Å2
Baniso -1Baniso -2Baniso -3
1-10.783 Å2-0 Å2-0 Å2
2---3.733 Å2-0 Å2
3----6.116 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6433 0 67 559 7059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0226623
X-RAY DIFFRACTIONf_angle_d1.2458990
X-RAY DIFFRACTIONf_chiral_restr0.231046
X-RAY DIFFRACTIONf_plane_restr0.0071149
X-RAY DIFFRACTIONf_dihedral_angle_d18.1782440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9310.2691100.2522167227781
1.931-1.9650.3161340.2382328246287
1.965-20.2521090.2252379248888
2-2.0390.2661400.2172446258690
2.039-2.080.2541280.2022446257492
2.08-2.1260.2771320.1842491262392
2.126-2.1750.2521280.1822540266895
2.175-2.230.2261450.1762585273095
2.23-2.290.241330.182560269395
2.29-2.3570.2571520.182593274596
2.357-2.4330.2621420.1832657279997
2.433-2.520.2711200.1822633275397
2.52-2.6210.2311560.1792621277797
2.621-2.740.231420.1722680282298
2.74-2.8850.2481390.1752710284999
2.885-3.0650.251530.1742697285099
3.065-3.3020.2151540.1742718287299
3.302-3.6340.2211590.15827162875100
3.634-4.1590.1921410.14527832924100
4.159-5.2380.1671370.14628022939100
5.238-39.0180.2431500.1982905305598

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