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

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Basic information

Entry
Database: PDB / ID: 6bif
TitleCrystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 1-(4-amino-2-hydroxyphenyl)ethan-1-one
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / Purine Nucleoside Phosphorylase
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
1-(4-amino-2-hydroxyphenyl)ethan-1-one / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1-(4-amino-2-hydroxyphenyl)ethan-1-one
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
DepositionNov 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,21210
Polymers31,4351
Non-polymers7769
Water5,008278
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)96,63530
Polymers94,3063
Non-polymers2,32927
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 area11210 Å2
ΔGint-8 kcal/mol
Surface area31040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.800, 99.800, 99.800
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-586-

HOH

21A-661-

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) / Strain (production host): Lemo21 (DE3)
References: UniProt: A0A0U3AGT1, purine-nucleoside phosphorylase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-DSJ / 1-(4-amino-2-hydroxyphenyl)ethan-1-one


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
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 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.6→57.62 Å / Num. obs: 43879 / % possible obs: 100 % / Redundancy: 11.5 % / CC1/2: 1 / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3199 / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
xia2data reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXQ

5cxq


Resolution: 1.6→57.62 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.72
RfactorNum. reflection% reflection
Rfree0.1814 2153 4.91 %
Rwork0.1574 --
obs0.1585 43847 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→57.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 43 278 2471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112221
X-RAY DIFFRACTIONf_angle_d1.1573002
X-RAY DIFFRACTIONf_dihedral_angle_d13.6851321
X-RAY DIFFRACTIONf_chiral_restr0.067346
X-RAY DIFFRACTIONf_plane_restr0.006387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6003-1.63760.2861420.2682734X-RAY DIFFRACTION100
1.6376-1.67850.27661220.25732770X-RAY DIFFRACTION100
1.6785-1.72390.26061550.23462742X-RAY DIFFRACTION100
1.7239-1.77460.25941710.22152705X-RAY DIFFRACTION100
1.7746-1.83190.21751290.19832783X-RAY DIFFRACTION100
1.8319-1.89740.19511840.18282714X-RAY DIFFRACTION100
1.8974-1.97340.18931360.16862786X-RAY DIFFRACTION100
1.9734-2.06320.18021430.1572755X-RAY DIFFRACTION100
2.0632-2.1720.18611420.1492777X-RAY DIFFRACTION100
2.172-2.30810.17841540.14712753X-RAY DIFFRACTION100
2.3081-2.48630.18041240.1392797X-RAY DIFFRACTION100
2.4863-2.73650.18331300.14442793X-RAY DIFFRACTION100
2.7365-3.13240.16151380.14822828X-RAY DIFFRACTION100
3.1324-3.94640.17511570.1422812X-RAY DIFFRACTION100
3.9464-57.65690.14891260.14752945X-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)
16.67194.81141.46856.32393.44135.8452-0.1140.2685-1.07930.13150.2957-0.81310.63750.2439-0.18810.26740.02350.08660.1827-0.00730.338527.500911.580452.8047
23.1824-0.21130.37223.3805-1.32483.12820.11730.2531-0.6725-0.1921-0.09530.12580.5093-0.1763-0.04310.3385-0.06140.0390.207-0.07820.332911.74648.257946.7267
31.6509-0.5479-0.69040.86050.68722.3766-0.09470.0458-0.311-0.0191-0.01580.07850.2782-0.08620.13050.2247-0.03380.04850.1557-0.02120.248315.50215.301153.5234
42.32790.25470.40611.07360.35021.0995-0.04870.1748-0.0177-0.16140.02040.0484-0.0363-0.05830.02920.1775-0.02140.01840.14950.00210.124111.836630.152747.0337
51.2885-0.23860.40132.76112.06754.3463-0.05480.3966-0.0362-0.5182-0.08170.2393-0.0812-0.15940.07310.2661-0.0475-0.02840.2926-0.01240.16071.216125.684834.9292
61.8608-0.09880.53291.10950.39960.3894-0.01310.05390.0492-0.0852-0.07020.1311-0.0627-0.15460.09650.1795-0.0115-0.00270.1886-0.0180.15521.111531.509551.7084
76.1881-1.5653-6.31322.3453.07258.7749-0.18610.3227-0.3242-0.0686-0.03380.06570.2573-0.28310.2630.2111-0.0598-0.0520.2341-0.03250.2056-0.792215.929241.9988
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 54 )
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 169 )
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 258 )
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 285 )

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