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- PDB-8c25: purine nucleoside phosphorylase in complex with JS-375 -

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Basic information

Entry
Database: PDB / ID: 8c25
Titlepurine nucleoside phosphorylase in complex with JS-375
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-JU9 / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,62517
Polymers55,1352
Non-polymers1,49015
Water11,187621
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)85,05727
Polymers82,7023
Non-polymers2,35524
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9640 Å2
ΔGint-175 kcal/mol
Surface area26300 Å2
MethodPISA
2
B: Purine nucleoside phosphorylase
hetero molecules

B: Purine nucleoside phosphorylase
hetero molecules

B: Purine nucleoside phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,81824
Polymers82,7023
Non-polymers2,11621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area8200 Å2
ΔGint-170 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.120, 125.120, 125.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27567.391 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria)
References: UniProt: A0A045IAS2, purine-nucleoside phosphorylase

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Non-polymers , 5 types, 636 molecules

#2: Chemical ChemComp-JU9 / [(~{E})-2-[4-methoxy-2-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)sulfanyl]phenyl]ethenyl]phosphonic acid


Mass: 379.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N3O5PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 2M Sodium chloride, 100 mM Sodium acetate, pH 4.6

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Aug 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 180675 / % possible obs: 99.8 % / Redundancy: 19.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.264 / Rrim(I) all: 0.271 / Net I/σ(I): 12.83
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.56-1.652.729290160.3972.8421
1.65-1.771.776274790.7641.8211
1.77-1.911.173255410.9011.2031
1.91-2.090.7235880.9670.7181
2.09-2.330.449213010.9870.4611
2.33-2.690.296187670.9940.3031
2.69-3.30.153159150.9980.1571
3.3-4.650.073122720.9990.0751
4.65-4.6730.054679610.0561

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0267refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→44.28 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.466 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 1079 1.2 %RANDOM
Rwork0.15311 ---
obs0.15348 91714 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 mean: 17.735 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.56→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 88 621 4501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124127
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163868
X-RAY DIFFRACTIONr_angle_refined_deg1.6741.6355669
X-RAY DIFFRACTIONr_angle_other_deg0.5641.5418973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.6161037
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17810595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02768
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1691.8522177
X-RAY DIFFRACTIONr_mcbond_other2.1691.8522177
X-RAY DIFFRACTIONr_mcangle_it3.3722.7652732
X-RAY DIFFRACTIONr_mcangle_other3.3742.7652733
X-RAY DIFFRACTIONr_scbond_it3.0512.121950
X-RAY DIFFRACTIONr_scbond_other3.052.1211951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5773.082922
X-RAY DIFFRACTIONr_long_range_B_refined6.66829.9364543
X-RAY DIFFRACTIONr_long_range_B_other6.30326.4544312
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.56→1.599 Å
RfactorNum. reflection% reflection
Rfree0.345 79 -
Rwork0.368 6674 -
obs--99.27 %

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