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- PDB-5ko6: Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase... -

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Basic information

Entry
Database: PDB / ID: 5ko6
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase from Schistosoma mansoni in complex with cytosine and ribose-1-phosphate
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE
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
6-AMINOPYRIMIDIN-2(1H)-ONE / 1-O-phosphono-alpha-D-ribofuranose / Purine nucleoside phosphorylase / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsTorini, J.R. / Romanello, L. / Bird, L. / Owens, R. / Brandao-Neto, J. / Pereira, H.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/14223-9 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)474402/2013-4 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
DepositionJun 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / _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 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,7013
Polymers31,3591
Non-polymers3412
Water6,197344
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)95,1029
Polymers94,0783
Non-polymers1,0246
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9830 Å2
ΔGint-58 kcal/mol
Surface area30340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.640, 98.640, 98.640
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-626-

HOH

21A-671-

HOH

31A-725-

HOH

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Components

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


Mass: 31359.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0U3AGT1, UniProt: G4VP83*PLUS, purine-nucleoside phosphorylase
#2: Chemical ChemComp-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O
#3: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
a-D-Ribf1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Lithium chloride, 0.1 M Cadmium chloride hemi(pentahydrate), 0.1 M Sodium acetate 4.5 30 % v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.42→44.113 Å / Num. obs: 60417 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.42-1.469.11.6070.541100
6.35-44.1110.60.037199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data scaling
xia2data reduction
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CXQ

1cxq


Resolution: 1.42→44.113 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.39
RfactorNum. reflection% reflection
Rfree0.1785 2943 4.87 %
Rwork0.1619 --
obs0.1627 60379 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.42 Å2 / Biso mean: 25.063 Å2 / Biso min: 9.22 Å2
Refinement stepCycle: final / Resolution: 1.42→44.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 22 344 2544
Biso mean--32.56 35.99 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062245
X-RAY DIFFRACTIONf_angle_d0.9533049
X-RAY DIFFRACTIONf_chiral_restr0.084357
X-RAY DIFFRACTIONf_plane_restr0.006394
X-RAY DIFFRACTIONf_dihedral_angle_d18.599833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4201-1.44330.2651240.296927062830
1.4433-1.46820.31521540.279927452899
1.4682-1.49490.30011340.252226942828
1.4949-1.52370.261380.226326812819
1.5237-1.55480.22121350.210726962831
1.5548-1.58860.21491560.206627442900
1.5886-1.62550.20391240.193827052829
1.6255-1.66620.19651390.184427502889
1.6662-1.71120.20611450.178126802825
1.7112-1.76160.21271500.177327222872
1.7616-1.81850.19691360.172727042840
1.8185-1.88350.19861520.167127322884
1.8835-1.95890.17331400.160727192859
1.9589-2.0480.18361430.160127402883
2.048-2.1560.15781290.150327202849
2.156-2.29110.1731240.151827742898
2.2911-2.4680.16251470.156527382885
2.468-2.71630.16511390.156327512890
2.7163-3.10920.18181410.151227672908
3.1092-3.91690.17231490.145127772926
3.9169-44.13440.14581440.147428913035
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)
16.6929-4.16392.69182.7813-1.37293.9980.08380.249-0.6618-0.1626-0.04160.45290.3933-0.3230.00890.1938-0.02230.07030.1654-0.02540.2363-27.6444-36.6056-4.7268
22.14220.53270.89412.46290.47552.9110.0951-0.1514-0.56870.2148-0.0726-0.04290.58920.1709-0.02760.27210.06950.03380.16870.04940.2788-12.0863-41.48392.721
31.8372-0.0322-0.43591.5097-0.77921.9061-0.0116-0.0346-0.27780.0841-0.02970.00250.13180.07920.03380.14540.01610.02270.1040.00120.1761-15.5933-34.2473-3.8423
41.9108-0.50620.17751.1057-0.18570.612-0.0856-0.17660.00840.19410.0563-0.0289-0.00230.03540.03020.13970.02410.00720.1086-0.00130.07-11.5368-19.62532.5781
51.01830.22270.41732.0218-1.45563.2853-0.0773-0.2875-0.02340.52310.0419-0.1746-0.13280.05390.02590.2750.0855-0.03330.23060.00010.1102-1.4893-23.945914.5877
61.90630.1887-0.12240.9138-0.48490.7272-0.0187-0.04920.06170.1177-0.0414-0.1062-0.06290.11190.06570.15190.0212-0.01250.14060.0090.1221-1.2432-18.2577-1.8766
74.69861.9682-4.43683.409-2.59036.0606-0.0580.0231-0.06910.17040.1830.09770.1839-0.2584-0.01460.20280.0878-0.06330.21280.04230.1633-0.3499-33.56338.1842
81.9999-2.51569.66492.0005-8.96364.1627-0.8959-2.8825-0.5927-0.01010.4130.06780.006-0.62960.49330.46910.6055-0.28120.82180.03490.07822.098-22.3631-4.697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 22 )A3 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 54 )A23 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 108 )A55 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 169 )A109 - 169
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 196 )A170 - 196
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 258 )A197 - 258
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 287 )A259 - 287
8X-RAY DIFFRACTION8chain 'A' and (resid 301 through 301 )A301

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