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- PDB-3e9r: Crystal structure of purine nucleoside phosphorylase from Schisto... -

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Basic information

Entry
Database: PDB / ID: 3e9r
TitleCrystal structure of purine nucleoside phosphorylase from Schistosoma mansoni in complex with adenine
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 / ADENINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsPereira, H.M. / Rezende, M.M. / Oliva, G. / Garratt, R.C.
CitationJournal: 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.
History
DepositionAug 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 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)94,46413
Polymers93,5923
Non-polymers87210
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-56.8 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.989, 119.995, 130.982
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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, 778 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#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: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
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: 1.2 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.85→45.88 Å / Num. obs: 66688 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.078 / Rsym value: 0.078
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.953.90.36523781195880.36599.3
1.95-2.0740.2343.13620390430.23499.4
2.07-2.2140.1813.43441085660.18199.8
2.21-2.394.10.1285.53293679870.12899.9
2.39-2.624.20.1026.73142874210.102100
2.62-2.934.30.0887.22903267420.088100
2.93-3.384.30.0748.22560859490.074100
3.38-4.144.30.0579.82187551150.057100
4.14-5.854.20.04911.21687439900.049100
5.85-45.883.90.04911.3902922870.04998.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.03 Å44.24 Å
Translation2.03 Å44.24 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TD1

1td1


Resolution: 1.85→41.029 Å / Occupancy max: 1 / Occupancy min: 0.01 / SU ML: 0.21 / σ(F): 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.201 3266 5.06 %
Rwork0.162 --
obs0.164 64600 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.03 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 162.89 Å2 / Biso mean: 29.968 Å2 / Biso min: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.506 Å2-0 Å2-0 Å2
2---4.708 Å2-0 Å2
3----2.428 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6388 0 50 768 7206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126544
X-RAY DIFFRACTIONf_angle_d1.1118867
X-RAY DIFFRACTIONf_chiral_restr0.0731035
X-RAY DIFFRACTIONf_plane_restr0.0061139
X-RAY DIFFRACTIONf_dihedral_angle_d16.7612378
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.8780.2551280.2232470259889
1.878-1.9070.2431360.2062416255290
1.907-1.9380.2341370.2052547268493
1.938-1.9720.2251180.1972492261092
1.972-2.0070.251270.1932565269295
2.007-2.0460.2231350.1812608274395
2.046-2.0880.241280.2242510263892
2.088-2.1330.2421280.1712556268492
2.133-2.1830.1951440.1592629277397
2.183-2.2370.2161590.1492666282598
2.237-2.2980.1971250.1512676280198
2.298-2.3660.1951320.1532708284098
2.366-2.4420.2091680.1552699286799
2.442-2.5290.211500.1582692284299
2.529-2.6310.2311480.1622726287499
2.631-2.750.1961740.162715288999
2.75-2.8950.2241460.1627562902100
2.895-3.0760.2151410.16427742915100
3.076-3.3140.181230.15627742897100
3.314-3.6470.2071400.14228012941100
3.647-4.1740.1681550.13228032958100
4.174-5.2580.1471700.13428313001100
5.258-41.0390.2021540.1842920307498

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