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

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Basic information

Entry
Database: PDB / ID: 5tbt
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Cytidine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE
Function / homology
Function and homology information


guanosine phosphorylase activity / 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
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 Å
AuthorsFaheem, M. / Torini, J.R. / Romanello, L. / 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
DepositionSep 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Apr 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 1.4Oct 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

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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)31,6993
Polymers31,3591
Non-polymers3392
Water3,963220
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)95,0969
Polymers94,0783
Non-polymers1,0186
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
Buried area9910 Å2
ΔGint-106 kcal/mol
Surface area30460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.153, 100.153, 100.153
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-554-

HOH

21A-581-

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) / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo
References: UniProt: A0A0U3AGT1, purine-nucleoside phosphorylase
#2: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE / Cytidine


Mass: 243.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N3O5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M ammonium acetate, 0.1M Bis-tris pH 6.5, 30% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→57.823 Å / Num. obs: 19849 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.194 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.1-2.1671.5170.5981100
8.91-57.826.50.0520.998198.8

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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: 5CXS

5cxs


Resolution: 2.101→57.823 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.93
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1026 5.18 %Random Selection
Rwork0.1904 ---
obs0.1922 19795 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.22 Å2 / Biso mean: 34.756 Å2 / Biso min: 16.15 Å2
Refinement stepCycle: final / Resolution: 2.101→57.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 22 220 2406
Biso mean--55.88 40.55 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022227
X-RAY DIFFRACTIONf_angle_d0.6043022
X-RAY DIFFRACTIONf_chiral_restr0.047354
X-RAY DIFFRACTIONf_plane_restr0.004390
X-RAY DIFFRACTIONf_dihedral_angle_d12.6691338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1007-2.21150.28061670.254126222789100
2.2115-2.350.29671390.238726562795100
2.35-2.53150.25881280.231226792807100
2.5315-2.78620.2581410.215926682809100
2.7862-3.18940.26071580.203526442802100
3.1894-4.01810.21451540.175727042858100
4.0181-57.84530.16651390.1532796293599
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)
18.8117-4.0489-0.32935.54520.37665.58340.1317-0.28620.56550.0325-0.0448-0.8787-0.57730.7751-0.19810.2291-0.0442-0.0050.31830.01230.3681113.3131203.085178.2202
24.57232.8328-0.57116.7542-1.83913.51380.0456-0.0636-0.2466-0.5458-0.1781-0.89550.24060.76490.07880.34660.0850.10530.43670.02320.3863115.9163185.122469.6647
31.2840.35460.08232.5280.85090.79-0.0187-0.015-0.15150.0450.0202-0.44880.11670.4799-0.03630.23930.06590.03010.41410.02360.3896115.5596190.067778.13
40.76631.4353-0.9133.4008-2.58543.8997-0.03630.1216-0.23250.01470.0397-0.14940.01620.0497-0.0410.2090.02680.00250.24720.00960.303104.5662192.211180.4924
51.0465-0.3335-0.2672.52360.50540.53760.00930.1867-0.0244-0.2026-0.0005-0.00820.02120.0354-0.01920.23030.0221-0.01030.24510.02010.166695.0222187.398872.4492
62.53230.8478-1.62798.03342.51967.43560.4841.0236-0.0424-1.1504-0.59090.16320.0288-0.57280.01080.42780.1212-0.00430.4723-0.02880.139100.7237179.776656.0312
71.49650.0873-0.87630.8143-0.34942.57130.0440.2181-0.2165-0.2195-0.1025-0.02560.20120.03990.05980.230.05280.01280.2145-0.05010.195392.8812173.390873.9233
81.18170.3637-0.27873.9773-0.13770.2958-0.06970.0772-0.1251-0.01470.0580.12350.0586-0.09790.0420.2310.03390.02240.2379-0.01810.17995.5158177.604774.8822
92.56161.9685-2.69442.6083-2.5897.6358-0.11860.1668-0.06820.0299-0.0451-0.4354-0.2431-0.00920.1590.27930.11190.00920.2725-0.07290.2735108.7235175.766666.8159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 23 )A5 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 47 )A24 - 47
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 84 )A48 - 84
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 108 )A85 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 169 )A109 - 169
6X-RAY DIFFRACTION6chain 'A' and (resid 170 through 182 )A170 - 182
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 213 )A183 - 213
8X-RAY DIFFRACTION8chain 'A' and (resid 214 through 258 )A214 - 258
9X-RAY DIFFRACTION9chain 'A' and (resid 259 through 287 )A259 - 287

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