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- PDB-3fb1: Crystal Structure of Purine Nucleoside Phosphorylase in Complex w... -

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Basic information

Entry
Database: PDB / ID: 3fb1
TitleCrystal Structure of Purine Nucleoside Phosphorylase in Complex with Ribose-1-Phosphate
ComponentsPurine-nucleoside phosphorylase
KeywordsTRANSFERASE / Purine nucleoside phsophorylase / ribose-1-phosphate / Glycosyltransferase
Function / homology
Function and homology information


guanosine phosphorylase activity / nucleoside metabolic process / 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 / 1-O-phosphono-alpha-D-ribofuranose / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.002 Å
AuthorsPereira, H.M. / Garratt, R.C. / Oliva, G.
Citation
Journal: J.Synchrotron Radiat. / Year: 2011
Title: Purine nucleoside phosphorylase from Schistosoma mansoni in complex with ribose-1-phosphate.
Authors: D'Muniz Pereira, H. / 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 1.2Jan 25, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)94,4599
Polymers93,5923
Non-polymers8676
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-68 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.965, 117.669, 129.514
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: Sugar ChemComp-R1P / 1-O-phosphono-alpha-D-ribofuranose / RIBOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-ribose / 1-O-phosphono-D-ribose / 1-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 18-20% PEG1500, 20% glycerol, 32mM Sodium Acetate, pH 4.9-5.0, 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 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 2→87.092 Å / Num. all: 139649 / Num. obs: 48547 / % possible obs: 95.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.362
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.112.50.4521.51583063120.45286.7
2.11-2.242.50.2982.31558063230.29890.9
2.24-2.392.50.21931562861530.21994.2
2.39-2.582.70.1514.71581459280.15196.9
2.58-2.832.80.1096.51568155350.10997.8
2.83-3.163.10.0788.91546250570.07898.7
3.16-3.653.40.05512.11536445440.05599.5
3.65-4.473.50.03915.81369839000.03999.5
4.47-6.323.50.03616.61072130370.03699.1
6.32-129.13.30.03515.4587117580.03597.8

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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
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.002→56.733 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.28 / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.234 2322 5.08 %
Rwork0.175 --
obs0.177 45735 89.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.688 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 142.72 Å2 / Biso mean: 35.763 Å2 / Biso min: 9.97 Å2
Baniso -1Baniso -2Baniso -3
1-9.421 Å20 Å2-0 Å2
2---3.07 Å2-0 Å2
3----6.351 Å2
Refinement stepCycle: LAST / Resolution: 2.002→56.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6337 0 54 368 6759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146504
X-RAY DIFFRACTIONf_angle_d1.2238815
X-RAY DIFFRACTIONf_chiral_restr0.071030
X-RAY DIFFRACTIONf_plane_restr0.0051127
X-RAY DIFFRACTIONf_dihedral_angle_d17.6242414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.002-2.0430.357990.2441946204568
2.043-2.0870.292990.2222056215573
2.087-2.1360.2291310.2042204233578
2.136-2.1890.241450.1842231237680
2.189-2.2480.2621190.1992341246083
2.248-2.3150.3071570.1942387254485
2.315-2.3890.31360.1762493262988
2.389-2.4750.2061370.1722555269290
2.475-2.5740.2491290.1772641277092
2.574-2.6910.2561550.1772627278293
2.691-2.8330.2521300.1752727285795
2.833-3.010.2271520.1712746289896
3.01-3.2430.2241460.1642807295397
3.243-3.5690.2021450.1552847299298
3.569-4.0850.1981300.1362903303399
4.085-5.1460.1581510.1352901305299
5.146-56.7560.2221610.1833001316297

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