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- PDB-6yjf: Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inh... -

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Basic information

Entry
Database: PDB / ID: 6yjf
TitlePlasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEGSmear at pH 6.5
ComponentsPhosphoglycerate kinase
KeywordsBIOSYNTHETIC PROTEIN / phosphoglycerate kinase / metabolic enzyme / kinase
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / gluconeogenesis / ADP binding / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature.
Similarity search - Domain/homology
Chem-OTQ / Phosphoglycerate kinase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsHyvonen, M. / Brear, P. / Blaszczyk, B.K.
CitationJournal: to be published
Title: Phosphoglycerate Kinase as a potential target for antimalarial therapy
Authors: King, L. / Brear, P. / Bourgard, C. / Cassiano, C. / Mota, D. / Blaszczyk, B.K. / Tomaz, K. / Khedim, M. / Furlan, M. / Ramos, P. / Andresen, E. / Tarczykowska, A. / Tiburcio, L. / Kurowska, ...Authors: King, L. / Brear, P. / Bourgard, C. / Cassiano, C. / Mota, D. / Blaszczyk, B.K. / Tomaz, K. / Khedim, M. / Furlan, M. / Ramos, P. / Andresen, E. / Tarczykowska, A. / Tiburcio, L. / Kurowska, A. / Sulskis, D. / Oliver, S. / Grotli, M. / Massirer, K. / Saphire, E. / Burmann, B. / Witkowski, B. / Costa, F. / Sunnerhagen, P. / Hyvonen, M. / Bilsland, E.
History
DepositionApr 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 2.0May 11, 2022Group: Database references / Non-polymer description / Structure summary
Category: chem_comp / database_2 / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight
Revision 2.1Jan 24, 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

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Assembly

Deposited unit
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6103
Polymers45,1991
Non-polymers4112
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint0 kcal/mol
Surface area18700 Å2
Unit cell
Length a, b, c (Å)42.594, 82.315, 124.495
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoglycerate kinase


Mass: 45199.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVC01_070025900, PVP01_0721000, PVT01_070026100 / Plasmid: pHAT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1G4HAR7, phosphoglycerate kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-OTQ / (2~{S})-2-(5-nitrofuran-2-yl)-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one


Mass: 319.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25 %v/v PEGSM, 0.1 M MES 6.5 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.85→68.66 Å / Num. obs: 34744 / % possible obs: 91.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 38.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.027 / Rrim(I) all: 0.098 / Net I/σ(I): 14.3 / Num. measured all: 448345
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.956.52.7272229034530.4661.1142.9690.663.9
5.86-68.6612.30.0431674513620.9990.0120.04545.5100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y3A

6y3a


Resolution: 1.85→25.05 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.913 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1665 4.87 %RANDOM
Rwork0.191 ---
obs0.193 34166 89.4 %-
Displacement parametersBiso max: 125.09 Å2 / Biso mean: 45.79 Å2 / Biso min: 27.17 Å2
Baniso -1Baniso -2Baniso -3
1--13.3692 Å20 Å20 Å2
2---2.353 Å20 Å2
3---15.7223 Å2
Refinement stepCycle: final / Resolution: 1.85→25.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 28 247 3443
Biso mean--53.86 53.67 -
Num. residues----416
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1213SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes481HARMONIC5
X-RAY DIFFRACTIONt_it3286HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion434SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4003SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3286HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4428HARMONIC21.16
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.6
LS refinement shellResolution: 1.85→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3633 84 4.86 %
Rwork0.3302 1643 -
all0.3318 1727 -
obs--53.3 %

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