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- PDB-7z4r: Plasmodium falciparum pyruvate kinase mutant - C343A -

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Basic information

Entry
Database: PDB / ID: 7z4r
TitlePlasmodium falciparum pyruvate kinase mutant - C343A
ComponentsPyruvate kinase
KeywordsTRANSFERASE / Redox regulation / glycolysis / malaria / drug-target
Function / homology
Function and homology information


Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding ...Glycolysis / Neutrophil degranulation / pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / protein homotetramerization / phosphorylation / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDillenberger, M. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)BE1540/23-2 Germany
CitationJournal: Structure / Year: 2022
Title: Prominent role of cysteine residues C49 and C343 in regulating Plasmodium falciparum pyruvate kinase activity.
Authors: Dillenberger, M. / Rahlfs, S. / Becker, K. / Fritz-Wolf, K.
History
DepositionMar 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 19, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.title
Revision 1.3May 1, 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: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8333
Polymers56,7701
Non-polymers632
Water3,135174
1
A: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
hetero molecules

A: Pyruvate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,33312
Polymers227,0794
Non-polymers2548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area13920 Å2
ΔGint-105 kcal/mol
Surface area73400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.420, 109.130, 134.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

21A-829-

HOH

31A-845-

HOH

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Components

#1: Protein Pyruvate kinase /


Mass: 56769.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue C343 is mutated to A / Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_0626800 / Production host: Escherichia coli (E. coli) / References: UniProt: C6KTA4, pyruvate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES, pH 6.5, 50 mM KCl, 10 mM MgCl2 and 14-24% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→32.3 Å / Num. obs: 162857 / % possible obs: 99.18 % / Redundancy: 3.7 % / Biso Wilson estimate: 49.89 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 16600 / CC1/2: 0.439 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292121472

Resolution: 2→32.3 Å / SU ML: 0.3698 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2483 3541 8 %
Rwork0.2146 40738 -
obs0.2172 44279 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.71 Å2
Refinement stepCycle: LAST / Resolution: 2→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3756 0 2 174 3932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293814
X-RAY DIFFRACTIONf_angle_d0.54645152
X-RAY DIFFRACTIONf_chiral_restr0.0441628
X-RAY DIFFRACTIONf_plane_restr0.0052657
X-RAY DIFFRACTIONf_dihedral_angle_d28.55691509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.45091430.46571654X-RAY DIFFRACTION99.83
2.03-2.060.48091370.41821576X-RAY DIFFRACTION99.65
2.06-2.090.40681420.37151623X-RAY DIFFRACTION99.6
2.09-2.120.37121420.34481631X-RAY DIFFRACTION99.83
2.12-2.150.36551390.32851622X-RAY DIFFRACTION99.6
2.15-2.190.36521390.31691606X-RAY DIFFRACTION99.77
2.19-2.230.34281420.27971626X-RAY DIFFRACTION100
2.23-2.270.31371420.27051633X-RAY DIFFRACTION99.83
2.27-2.320.28831410.26121620X-RAY DIFFRACTION99.77
2.32-2.370.32231420.2641639X-RAY DIFFRACTION99.61
2.37-2.430.30661400.26521603X-RAY DIFFRACTION99.83
2.43-2.490.30951410.25361623X-RAY DIFFRACTION99.55
2.49-2.550.29251420.26271633X-RAY DIFFRACTION99.94
2.55-2.630.33151420.24971637X-RAY DIFFRACTION99.61
2.63-2.710.29161410.22991621X-RAY DIFFRACTION99.6
2.71-2.810.29951400.2271614X-RAY DIFFRACTION99.1
2.81-2.920.32991410.23251623X-RAY DIFFRACTION99.1
2.92-3.060.26891410.23411613X-RAY DIFFRACTION98.21
3.06-3.220.25211410.22641627X-RAY DIFFRACTION98.77
3.22-3.420.26191410.23091624X-RAY DIFFRACTION98.77
3.42-3.680.22811420.21581623X-RAY DIFFRACTION98.33
3.68-4.050.25711430.19111654X-RAY DIFFRACTION98.52
4.05-4.640.17611420.16681626X-RAY DIFFRACTION98
4.64-5.840.22251430.18751650X-RAY DIFFRACTION98.03

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