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- PDB-3e0q: Crystal structure of Schistosoma mansoni purine nucleoside phosph... -

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Basic information

Entry
Database: PDB / ID: 3e0q
TitleCrystal structure of Schistosoma mansoni purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor
ComponentsPurine-nucleoside phosphorylase
KeywordsTRANSFERASE / Monocyclic inhibitor / Glycosyltransferase
Function / homology
Function and homology information


nucleoside metabolic process / guanosine phosphorylase activity / purine-nucleoside phosphorylase activity / purine-nucleoside phosphorylase / 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
Chem-JFD / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.9 Å
AuthorsPereira, H.M. / Berdini, V. / Ferri, M.R. / Cleasby, A. / Garratt, R.C.
Citation
Journal: Acta Trop. / Year: 2010
Title: Crystal structure of Schistosoma purine nucleoside phosphorylase complexed with a novel monocyclic inhibitor.
Authors: Pereira, H.M. / Berdini, V. / Ferri, M.R. / Cleasby, A. / 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
DepositionJul 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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)94,52210
Polymers93,5923
Non-polymers9317
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-55.1 kcal/mol
Surface area29830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.849, 120.018, 131.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-JFD / 6-amino-5-bromo-1,2,3,4-tetrahydropyrimidine-2,4-dione / 6-amino-5-bromopyrimidine-2,4(1H,3H)-dione


Mass: 205.997 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H4BrN3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / 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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 18-20% PEG 1500, 20% Glycerol, 32mM Sodium acetate, pH 4.9-5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 27, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→44.46 Å / Num. obs: 56943 / % possible obs: 94.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-22.30.4461.71842880680.44692.9
2-2.122.60.2922.72080881200.29298.7
2.12-2.272.60.1993.91943475330.19996.8
2.27-2.452.60.1495.11799169150.14996.2
2.45-2.692.60.1077.11660663410.10794.9
2.69-32.60.06910.81496156910.06994
3-3.472.60.04615.91326350070.04693.5
3.47-4.252.70.0322.41135342310.0393.1
4.25-6.012.70.02425.9877732370.02490.9
6.01-44.462.60.0259.6470018000.02588.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1TCV

1tcv


Resolution: 1.9→44.32 Å / Num. restraintsaints: 87047 / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.27 / σ(F): 1.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.236 2853 5.02 %
Rwork0.179 --
obs0.182 56886 93.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.161 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso max: 60.82 Å2 / Biso mean: 20.249 Å2 / Biso min: 5.34 Å2
Baniso -1Baniso -2Baniso -3
1-2.775 Å20 Å20 Å2
2--3.427 Å20 Å2
3---3.509 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 46 584 6940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126467
X-RAY DIFFRACTIONf_angle_d1.3098756
X-RAY DIFFRACTIONf_chiral_restr0.1751023
X-RAY DIFFRACTIONf_plane_restr0.0061122
X-RAY DIFFRACTIONf_dihedral_angle_d18.6532357
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9330.2981280.2392454258286
1.933-1.9680.2951310.2332651278293
1.968-2.0060.251440.2132779292398
2.006-2.0470.2871690.22781295099
2.047-2.0910.2621540.192796295097
2.091-2.140.2541510.182741289298
2.14-2.1930.2321500.1742776292696
2.193-2.2530.2671260.1742750287697
2.253-2.3190.2481530.1822701285496
2.319-2.3940.2641660.1822710287695
2.394-2.4790.2791300.1882732286296
2.479-2.5790.2811340.1842726286095
2.579-2.6960.2461360.1842708284494
2.696-2.8380.2381400.1722683282393
2.838-3.0160.2311440.1762694283893
3.016-3.2490.2271290.1692667279693
3.249-3.5750.2141520.1672665281792
3.575-4.0930.1721370.1522669280691
4.093-5.1550.1921430.1452690283391
5.155-44.320.2121360.1962660279685

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