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- PDB-3f8w: Crystal structure of Schistosoma mansoni purine nucleoside phosph... -

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Basic information

Entry
Database: PDB / ID: 3f8w
TitleCrystal structure of Schistosoma mansoni purine nucleoside phosphorylase in complex with adenosine
ComponentsPurine-nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase / Schistosoma / adenosine / 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
ADENOSINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsPereira, H.M. / Rezende, M.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 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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)94,91612
Polymers93,5923
Non-polymers1,3249
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-55.2 kcal/mol
Surface area29560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.715, 121.273, 133.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 4:61 or resseq 68:286)
21chain B and (resseq 4:61 or resseq 68:286)
31chain C and (resseq 4:61 or resseq 68:286)

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111AA4 - 614 - 61
121AA68 - 28668 - 286
211BB4 - 614 - 61
221BB68 - 28668 - 286
311CC4 - 614 - 61
321CC68 - 28668 - 286

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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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
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: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2.3→46.93 Å / Num. obs: 37280 / % possible obs: 100 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.128 / Rsym value: 0.128 / Net I/σ(I): 4.522
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.4213.20.5721.37060053460.572100
2.42-2.5713.20.4331.76719850720.433100
2.57-2.7513.20.3132.46317947710.313100
2.75-2.9713.30.2173.35941444780.217100
2.97-3.2513.30.1644.25460140980.164100
3.25-3.6413.30.1145.85009637600.114100
3.64-4.213.30.0916.54458433560.091100
4.2-5.1413.20.087.43730528210.08100
5.14-7.27130.087.62929922560.08100
7.27-46.9311.80.0658.51566413220.06599.6

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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
MAR345CCDdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TD1

1td1


Resolution: 2.3→46.009 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.26 / σ(F): 0.02 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.204 1763 4.97 %
Rwork0.174 --
obs0.176 35488 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.265 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 210.05 Å2 / Biso mean: 42.729 Å2 / Biso min: 8.07 Å2
Baniso -1Baniso -2Baniso -3
1-14.013 Å2-0 Å2-0 Å2
2---8.181 Å2-0 Å2
3----5.832 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6385 0 84 334 6803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156582
X-RAY DIFFRACTIONf_angle_d1.5478926
X-RAY DIFFRACTIONf_chiral_restr0.1021034
X-RAY DIFFRACTIONf_plane_restr0.0071137
X-RAY DIFFRACTIONf_dihedral_angle_d22.952421
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2088X-RAY DIFFRACTIONPOSITIONAL
12B2088X-RAY DIFFRACTIONPOSITIONAL0.09
13C2075X-RAY DIFFRACTIONPOSITIONAL0.083
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.3620.2071260.1782464259093
2.362-2.4320.2481280.1862393252192
2.432-2.510.2171220.1942468259093
2.51-2.60.2551220.1882546266895
2.6-2.7040.2441390.1852518265796
2.704-2.8270.231290.1812566269597
2.827-2.9760.2151410.1762596273798
2.976-3.1620.2261390.1792630276999
3.162-3.4070.1841270.1732634276199
3.407-3.7490.1911460.1592668281499
3.749-4.2910.1711310.14926982829100
4.291-5.4050.1721590.1527152874100
5.405-46.0090.2121540.1882829298398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.05280.20170.36141.26360.11010.61490.03520.12640.1618-0.3822-0.0857-0.1708-0.187-0.05550.03650.22460.02050.0160.10510.04640.190418.234837.898215.141
20.9541-0.1999-0.29261.09180.30631.1665-0.01790.018-0.02410.008-0.0306-0.08040.38260.01560.08680.1690.0150.03510.0901-0.00380.088322.77191.156718.3113
30.9827-0.4944-0.14051.45070.14161.2855-0.0838-0.07990.1170.37320.09-0.1283-0.0766-0.01350.02710.17630.0169-0.05790.1387-0.04090.122318.720222.137748.7712
40.314-0.06220.08450.619-0.04680.6578-0.02080.03670.04560.0063-0.0026-0.0738-0.0051-0.02540.0120.117-0.0169-0.00260.1975-0.00170.203917.662719.472426.379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain S

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