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

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Basic information

Entry
Database: PDB / ID: 5tbs
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with adenine
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE
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
ADENINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFaheem, M. / Torini, J.R. / Romanello, L. / Brandao-Neto, J. / Pereira, H.M.
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 1.2Oct 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)31,7295
Polymers31,3591
Non-polymers3704
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)95,18715
Polymers94,0783
Non-polymers1,10912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_656-z+3/2,-x,y+3/21
crystal symmetry operation10_536-y,z-3/2,-x+3/21
Buried area10690 Å2
ΔGint-14 kcal/mol
Surface area31480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.827, 100.827, 100.827
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-547-

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) / Gene: Smp_179110 / Plasmid: pOPINS3C / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo
References: UniProt: A0A0U3AGT1, purine-nucleoside phosphorylase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H5N5
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
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% PEG 3350

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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: 1.9→50.414 Å / Num. obs: 27201 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 26.01 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.947.80.8451100
9.11-71.36.80.0151100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
xia2data reduction
xia2data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CXS

5cxs


Resolution: 1.9→50.414 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.55
RfactorNum. reflection% reflectionSelection details
Rfree0.1968 1343 4.95 %Random selection
Rwork0.1582 ---
obs0.16 27154 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 102.78 Å2 / Biso mean: 32.8235 Å2 / Biso min: 11.33 Å2
Refinement stepCycle: final / Resolution: 1.9→50.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 12 233 2423
Biso mean--35.84 40.12 -
Num. residues----285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152229
X-RAY DIFFRACTIONf_angle_d1.2053023
X-RAY DIFFRACTIONf_chiral_restr0.08351
X-RAY DIFFRACTIONf_plane_restr0.008392
X-RAY DIFFRACTIONf_dihedral_angle_d12.8991344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.96790.35751470.314325022649
1.9679-2.04670.24031420.202725502692
2.0467-2.13990.21881470.177625392686
2.1399-2.25270.2341420.176725552697
2.2527-2.39380.2691410.18825382679
2.3938-2.57870.20721210.154126082729
2.5787-2.83810.16481390.147825452684
2.8381-3.24880.19371190.146726342753
3.2488-4.09280.16781160.137426222738
4.0928-50.43120.15941290.14227182847
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)
11.26090.8675-0.73294.52271.23451.2475-0.1278-0.0307-0.15820.0630.1182-0.56160.12640.38190.02230.21190.0019-0.06290.31010.03160.3376113.0888-97.113675.069
20.8638-0.3929-0.18291.4319-0.46242.5696-0.03190.02160.13470.0841-0.0057-0.6137-0.40320.75420.03070.2376-0.1023-0.04730.37740.00670.4788117.277-88.319974.3711
31.012-1.34951.15942.2942-2.05212.5923-0.04660.01840.11050.09810.0208-0.2811-0.16340.08450.050.1698-0.0216-0.02640.18860.0180.235105.0465-92.249270.2131
41.1740.17890.44811.4081-0.06580.91680.0091-0.17290.13790.2794-0.0711-0.0233-0.1787-0.00290.06010.1932-0.0398-0.00410.1666-0.00490.127595.795-80.684778.6805
51.9818-1.06991.12952.1925-1.81955.00060.044-0.0984-0.0640.1513-0.0589-0.3224-0.08020.22250.02430.3158-0.104-0.07870.2589-0.05360.2857109.1945-74.971782.9072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 38 )A3 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 84 )A39 - 84
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 108 )A85 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 258 )A109 - 258
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 442 )A259 - 442

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