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- PDB-7zsq: human purine nucleoside phosphorylase in complex with JS-555 -

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Basic information

Entry
Database: PDB / ID: 7zsq
Titlehuman purine nucleoside phosphorylase in complex with JS-555
ComponentsPurine nucleoside phosphorylase
KeywordsTRANSFERASE / PNP-inhibitor complex
Function / homology
Function and homology information


nucleoside metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / cytoplasm
Similarity search - Function
Putative purine nucleotide phosphorylase / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Purine nucleoside phosphorylase / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Chem-JTO / polyethylene glycol / DI(HYDROXYETHYL)ETHER / 6-tungstotellurate(VI) / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsDjukic, S. / Pachl, P. / Rezacova, P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729European Union
CitationJournal: J.Med.Chem. / Year: 2023
Title: Design, Synthesis, Biological Evaluation, and Crystallographic Study of Novel Purine Nucleoside Phosphorylase Inhibitors.
Authors: Skacel, J. / Djukic, S. / Baszczynski, O. / Kalcic, F. / Bilek, T. / Chalupsky, K. / Kozak, J. / Dvorakova, A. / Tloust'ova, E. / Kral'ova, Z. / Smidkova, M. / Voldrich, J. / Rumlova, M. / ...Authors: Skacel, J. / Djukic, S. / Baszczynski, O. / Kalcic, F. / Bilek, T. / Chalupsky, K. / Kozak, J. / Dvorakova, A. / Tloust'ova, E. / Kral'ova, Z. / Smidkova, M. / Voldrich, J. / Rumlova, M. / Pachl, P. / Brynda, J. / Vuckova, T. / Fabry, M. / Snasel, J. / Pichova, I. / Rezacova, P. / Mertlikova-Kaiserova, H. / Janeba, Z.
History
DepositionMay 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase
B: Purine nucleoside phosphorylase
C: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,77111
Polymers83,1743
Non-polymers3,5988
Water7,512417
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.070, 90.930, 143.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 27724.584 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: deoD, E5M05_03615, E5M23_14660, E5M52_18960, E5M78_19105, ERS013440_01955, ERS027646_00621, ERS027659_03654, SAMEA2683035_02840
Production host: Escherichia coli (E. coli)
References: UniProt: A0A045IAS2, purine-nucleoside phosphorylase

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Non-polymers , 7 types, 425 molecules

#2: Chemical ChemComp-JTO / [2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]phenoxy]methylphosphonic acid


Mass: 353.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H12N3O5PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O24TeW6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 30.00 % v/v Polyethylene glycol 400; 100 mM HEPES; pH 7.5; 200 mM Magnesium chloride; 1 mM TEW

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.77→48.38 Å / Num. obs: 140249 / % possible obs: 99.9 % / Redundancy: 6.96 % / Biso Wilson estimate: 34.629 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.161 / Rrim(I) all: 0.174 / Χ2: 0.887 / Net I/σ(I): 8.39 / Num. measured all: 976139
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.77-1.887.1872.5150.6216241622700225990.2532.7199.6
1.88-2.017.1571.3971.2415249421311213080.5321.505100
2.01-2.176.9530.7842.3113818619879198750.7730.847100
2.17-2.376.6550.443412148518256182550.9070.48100
2.37-2.656.8790.2736.5311381116545165440.9670.295100
2.65-3.067.210.15311.8410487214545145450.990.165100
3.06-3.746.8590.08520.018455312327123270.9970.093100
3.74-5.286.490.0531.0861832952895280.9980.055100
5.28-48.386.9270.04336.9436490527752680.9990.04799.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g2o

1g2o


Resolution: 1.77→48.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.547 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1099 1.5 %RANDOM
Rwork0.1819 ---
obs0.1823 72306 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.63 Å2 / Biso mean: 30.516 Å2 / Biso min: 17.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 1.77→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5697 0 141 417 6255
Biso mean--35.15 36.85 -
Num. residues----790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135966
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155723
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.6578232
X-RAY DIFFRACTIONr_angle_other_deg1.3691.56513102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81920.483269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49715834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0631550
X-RAY DIFFRACTIONr_chiral_restr0.0730.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021253
LS refinement shellResolution: 1.77→1.815 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.37 79 -
Rwork0.362 5239 -
obs--99.38 %

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