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

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Basic information

Entry
Database: PDB / ID: 5tbu
TitleCrystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with Hypoxanthine
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
HYPOXANTHINE / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7305
Polymers31,3591
Non-polymers3714
Water4,071226
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)95,19015
Polymers94,0783
Non-polymers1,11212
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area10970 Å2
ΔGint-12 kcal/mol
Surface area30830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.708, 99.708, 99.708
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-553-

HOH

21A-611-

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-HPA / HYPOXANTHINE


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#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.: 226 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
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→57.566 Å / Num. obs: 19582 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.92 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.164.70.851199.1
8.91-70.57.70.0441100

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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: 2.1→57.566 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.49
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 902 4.61 %Random selection
Rwork0.1887 ---
obs0.1904 19553 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.33 Å2 / Biso mean: 25.2581 Å2 / Biso min: 8.61 Å2
Refinement stepCycle: final / Resolution: 2.1→57.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 22 226 2412
Biso mean--19.98 31.86 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022228
X-RAY DIFFRACTIONf_angle_d0.5243021
X-RAY DIFFRACTIONf_chiral_restr0.046351
X-RAY DIFFRACTIONf_plane_restr0.004391
X-RAY DIFFRACTIONf_dihedral_angle_d13.1051343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1002-2.23170.29071580.24713059321799
2.2317-2.40410.26261580.215130533211100
2.4041-2.6460.21261550.205430813236100
2.646-3.02890.2351500.195430923242100
3.0289-3.81590.22571560.17731143270100
3.8159-57.5880.19421250.162632523377100
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)
12.6005-1.56870.48815.27430.51232.5345-0.13810.01020.7364-0.37440.1282-0.5282-0.51160.2658-0.00850.2486-0.05180.00490.19160.00090.314427.5501-12.5202-3.2154
21.826-0.3902-0.72251.2968-0.89031.61280.0631-0.15140.6838-0.084-0.08730.0894-0.5326-0.14730.00610.33510.0158-0.05780.2047-0.07310.399911.3371-8.31582.9977
31.19640.1017-0.31921.00870.00921.2278-0.0310.03860.2773-0.1842-0.05880.2158-0.4012-0.12560.06070.29140.0149-0.05210.1944-0.03190.361313.8432-10.8399-2.0397
42.71191.31422.44890.66331.13522.31280.0378-0.11180.26960.0535-0.06480.20020.0764-0.1294-0.00870.1743-0.0045-0.01890.1525-0.01040.209916.4664-20.7697-5.2135
50.93170.08570.09830.6950.41230.5482-0.0249-0.14370.03450.09780.03080.06050.0325-0.0353-0.00390.13590.0115-0.00790.156-0.00290.133511.7532-30.20992.9606
60.99310.326-0.20791.59431.292.21290.1102-0.25390.03910.265-0.19320.14380.0693-0.39860.06040.19820.04580.02280.2905-0.00730.1730.7791-25.869714.898
70.95050.09350.00690.61480.33810.57810.0103-0.0257-0.05550.0249-0.06750.09510.0565-0.10970.05960.13060.00010.01320.1598-0.00960.14880.6877-31.7529-1.7588
81.44820.81821.47951.12110.83913.9708-0.1418-0.24710.35380.071-0.09520.0307-0.2274-0.25590.21280.18490.06070.02250.2172-0.05860.20830.167-16.2068.6364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 22 )A5 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 54 )A23 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 84 )A55 - 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 196 )A170 - 196
7X-RAY DIFFRACTION7chain 'A' and (resid 197 through 258 )A197 - 258
8X-RAY DIFFRACTION8chain 'A' and (resid 259 through 287 )A259 - 287

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