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- PDB-5cxq: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase... -

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Basic information

Entry
Database: PDB / ID: 5cxq
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase from Schistosoma mansoni in APO form
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity
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
Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsTorini, J.R. / Romanello, L. / Bird, L. / Owens, R. / Brandao-Neto, J. / Pereira, H.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
CitationJournal: PLoS ONE / Year: 2018
Title: The molecular structure of Schistosoma mansoni PNP isoform 2 provides insights into the nucleoside selectivity of PNPs.
Authors: Torini, J.R. / Romanello, L. / Batista, F.A.H. / Serrao, V.H.B. / Faheem, M. / Zeraik, A.E. / Bird, L. / Nettleship, J. / Reddivari, Y. / Owens, R. / DeMarco, R. / Borges, J.C. / Brandao-Neto, J. / Pereira, H.D.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase


Theoretical massNumber of molelcules
Total (without water)31,4561
Polymers31,4561
Non-polymers00
Water5,242291
1
A: Purine nucleoside phosphorylase

A: Purine nucleoside phosphorylase

A: Purine nucleoside phosphorylase


Theoretical massNumber of molelcules
Total (without water)94,3693
Polymers94,3693
Non-polymers00
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 area7420 Å2
ΔGint-56 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.550, 99.550, 99.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-499-

HOH

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Components

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


Mass: 31456.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_179110 / Plasmid: pOPINS3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): Lemo 21
References: UniProt: G4VP83, purine-nucleoside phosphorylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 8000, 20% ethylene glycol, 30mM Sodium fluoride, 30mM sodium bromide, 30mM sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.57→44.52 Å / Num. all: 46089 / Num. obs: 46089 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 18.79 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-IDRejects% possible all
1.57-1.6170.66610100
7.02-44.526.60.0421099.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FAZ

3faz


Resolution: 1.57→44.52 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 2329 5.06 %Random
Rwork0.1848 43721 --
obs0.1862 46050 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.96 Å2 / Biso mean: 27.1104 Å2 / Biso min: 5.46 Å2
Refinement stepCycle: final / Resolution: 1.57→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 0 291 2462
Biso mean---38.31 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072219
X-RAY DIFFRACTIONf_angle_d1.0873011
X-RAY DIFFRACTIONf_chiral_restr0.046352
X-RAY DIFFRACTIONf_plane_restr0.005391
X-RAY DIFFRACTIONf_dihedral_angle_d12.287832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5703-1.60240.25481430.238725722715
1.6024-1.63720.2711230.223525712694
1.6372-1.67530.22561480.215925002648
1.6753-1.71720.2771400.216525852725
1.7172-1.76360.24021060.206725152621
1.7636-1.81550.22031290.206625622691
1.8155-1.87410.22921220.205826012723
1.8741-1.94110.26281190.206325302649
1.9411-2.01880.23121400.198225682708
2.0188-2.11070.21791530.190125602713
2.1107-2.2220.21781520.184625342686
2.222-2.36120.20161370.18425902727
2.3612-2.54350.22451420.194825432685
2.5435-2.79940.20621520.185525882740
2.7994-3.20440.20621360.185125852721
3.2044-4.03670.21371450.16926112756
4.0367-44.5380.17551420.162527062848
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)
11.4909-0.6852-0.36140.9201-0.12691.18030.13660.159-0.7168-0.0534-0.09370.04280.4669-0.0814-0.04920.301-0.01640.01340.2038-0.05140.338517.788110.394448.0343
20.927-0.2209-0.17630.5160.06510.7974-0.007-0.0359-0.31620.02090.01330.07330.2843-0.1169-0.01730.2196-0.02290.0190.1457-0.01160.259515.676813.99653.7582
31.02750.25390.16610.91740.34760.7798-0.0560.16410.0053-0.17650.01210.1015-0.0251-0.12940.04320.156-0.0226-0.01230.14920.00380.1035.467729.757146.5413
42.3951-0.0676-1.29811.37810.20812.4673-0.06060.1362-0.3117-0.14150.0075-0.04010.0959-0.05690.08740.227-0.0825-0.04290.2271-0.04660.19150.679115.974141.1349
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 47 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 108 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 258 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 287 )A0

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