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- PDB-6bb7: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 fr... -

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Basic information

Entry
Database: PDB / ID: 6bb7
TitleCrystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 3-methyl-1,2-dihydropyridin-2-one
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE/INHIBITOR / Purine Nucleoside Phosphorylase / TRANSFERASE / TRANSFERASE-INHIBITOR complex
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
3-methylpyridin-2-ol / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsFaheem, M. / Neto, J.B. / Collins, P. / Pearce, N.M. / Valadares, N.F. / Bird, L. / Pereira, H.M. / Delft, F.V. / Barbosa, J.A.R.G.
CitationJournal: To Be Published
Title: Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 3-methylpyridin-1-ium-2-olate
Authors: Faheem, M. / Neto, J.B. / Collins, P. / Pearce, N.M. / Valadares, N.F. / Bird, L. / Pereira, H.M. / Delft, F.V. / Barbosa, J.A.R.G.
History
DepositionOct 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8576
Polymers31,4351
Non-polymers4225
Water4,197233
1
A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules

A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,57118
Polymers94,3063
Non-polymers1,26515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_456z-1/2,-x+1/2,-y+11
crystal symmetry operation12_565-y+1/2,-z+1,x+1/21
Buried area9340 Å2
ΔGint-40 kcal/mol
Surface area31540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.110, 100.110, 100.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-566-

HOH

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Components

#1: Protein Purine nucleoside phosphorylase / Inosine-guanosine phosphorylase


Mass: 31435.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U3AGT1, 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-D4V / 3-methylpyridin-2-ol / (R)-N-[2-[1-(AMINOIMINOMETHYL)-3-PIPERIDINYL]-1-OXOETHYL]-4-(PHENYLETHYNYL)-L-PHENYLALANINE METHYL ESTER


Mass: 109.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M Ammonium Acetate , 0.1 M Bis-Tris, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.44→50.06 Å / Num. obs: 60595 / % possible obs: 100 % / Redundancy: 11.2 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4441 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXQ

5cxq


Resolution: 1.44→50.055 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 2983 4.93 %
Rwork0.1662 --
obs0.1667 60554 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→50.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 24 233 2394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012203
X-RAY DIFFRACTIONf_angle_d1.0562985
X-RAY DIFFRACTIONf_dihedral_angle_d16.94810
X-RAY DIFFRACTIONf_chiral_restr0.088348
X-RAY DIFFRACTIONf_plane_restr0.007385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.46360.33181460.29272712X-RAY DIFFRACTION100
1.4636-1.48890.29121440.26712696X-RAY DIFFRACTION100
1.4889-1.51590.28361420.25482732X-RAY DIFFRACTION100
1.5159-1.54510.28911340.2212735X-RAY DIFFRACTION100
1.5451-1.57660.21861490.20652710X-RAY DIFFRACTION100
1.5766-1.61090.20271230.19042725X-RAY DIFFRACTION100
1.6109-1.64840.20241520.18742730X-RAY DIFFRACTION100
1.6484-1.68960.20841230.17952688X-RAY DIFFRACTION100
1.6896-1.73530.18791550.1842765X-RAY DIFFRACTION100
1.7353-1.78640.18231690.17242696X-RAY DIFFRACTION100
1.7864-1.8440.18411260.15912720X-RAY DIFFRACTION100
1.844-1.910.16621840.15482678X-RAY DIFFRACTION100
1.91-1.98640.17471320.15952742X-RAY DIFFRACTION100
1.9864-2.07680.1781400.15952748X-RAY DIFFRACTION100
2.0768-2.18630.1861430.15762748X-RAY DIFFRACTION100
2.1863-2.32330.17121540.15482730X-RAY DIFFRACTION100
2.3233-2.50270.17311200.15192780X-RAY DIFFRACTION100
2.5027-2.75450.18081320.16222773X-RAY DIFFRACTION100
2.7545-3.15310.17471360.16332775X-RAY DIFFRACTION100
3.1531-3.97230.17961550.1612762X-RAY DIFFRACTION100
3.9723-50.08520.14141240.16212926X-RAY DIFFRACTION100
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)
12.87574.3331.38728.62272.41123.03470.01060.1534-1.05660.20920.1681-0.51240.84670.3313-0.20090.310.03590.02120.1789-0.0510.425127.634611.816853.0554
22.53180.12481.56711.2186-0.38344.15040.11110.0575-0.5207-0.06140.0307-0.00640.6249-0.266-0.13010.3585-0.07550.03780.1899-0.04510.385913.12199.455849.5339
36.3622-4.0788-7.07892.82224.84878.5160.01360.2003-0.4261-0.0574-0.16330.11140.0461-0.28380.13080.1991-0.0160.02730.12790.00030.20416.871720.796655.5378
44.43-3.5011-1.70924.9531.91032.94090.0730.26220.0921-0.3215-0.10350.2067-0.0502-0.30930.03290.1876-0.0545-0.03290.18670.00380.14031.731826.274744.2405
51.44310.30570.05290.93060.36480.6798-0.05420.20890.0218-0.19250.00290.10.0113-0.1560.05280.1975-0.0315-0.00350.19550.00020.14356.187130.564747.2124
64.6398-0.8458-3.68252.46292.31217.5984-0.17250.2314-0.36640.0152-0.0246-0.02810.3091-0.22960.24190.2958-0.0911-0.04810.2632-0.03650.2476-0.73316.042542.3034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 258 )
6X-RAY DIFFRACTION6chain 'A' and (resid 259 through 285 )

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