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- PDB-7z4n: Plasmodium falciparum pyruvate kinase complexed with pyruvate -

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Basic information

Entry
Database: PDB / ID: 7z4n
TitlePlasmodium falciparum pyruvate kinase complexed with pyruvate
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
: / DI(HYDROXYETHYL)ETHER / PYRUVIC ACID / Pyruvate kinase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1May 1, 2024Group: Refinement description / Category: 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)58,44418
Polymers56,8021
Non-polymers1,64217
Water2,900161
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)233,77672
Polymers227,2084
Non-polymers6,56868
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 area33120 Å2
ΔGint14 kcal/mol
Surface area70320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.890, 112.400, 131.970
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-743-

HOH

21A-796-

HOH

31A-811-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pyruvate kinase /


Mass: 56801.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_0626800 / Production host: Escherichia coli (E. coli) / References: UniProt: C6KTA4, pyruvate kinase

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Non-polymers , 7 types, 178 molecules

#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: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: Aug 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→36.2 Å / Num. obs: 53978 / % possible obs: 97.59 % / Redundancy: 3.3 % / Biso Wilson estimate: 35.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0597 / Net I/σ(I): 10.6
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 16185 / CC1/2: 0.511

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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: 1.8→36.2 Å / SU ML: 0.3379 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2447 3237 6 %
Rwork0.205 50722 -
obs0.2073 53959 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 105 161 4032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01443920
X-RAY DIFFRACTIONf_angle_d1.35295266
X-RAY DIFFRACTIONf_chiral_restr0.078632
X-RAY DIFFRACTIONf_plane_restr0.0104663
X-RAY DIFFRACTIONf_dihedral_angle_d28.4502568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.54061400.52092196X-RAY DIFFRACTION98.48
1.83-1.860.47681380.46242165X-RAY DIFFRACTION97.58
1.86-1.890.47361390.40932178X-RAY DIFFRACTION97.72
1.89-1.920.42631410.34472209X-RAY DIFFRACTION98.57
1.92-1.950.32531420.30762214X-RAY DIFFRACTION98.74
1.95-1.990.39611410.26762217X-RAY DIFFRACTION99.03
1.99-2.030.3461420.25822222X-RAY DIFFRACTION98.62
2.03-2.080.31411390.23412189X-RAY DIFFRACTION98.6
2.08-2.120.30411400.22732203X-RAY DIFFRACTION98.12
2.12-2.180.25061410.22392199X-RAY DIFFRACTION98.32
2.18-2.240.25741400.22712203X-RAY DIFFRACTION98.12
2.24-2.30.30431400.21882194X-RAY DIFFRACTION98.44
2.3-2.380.27981430.20982233X-RAY DIFFRACTION98.79
2.38-2.460.23751420.20032220X-RAY DIFFRACTION98.58
2.46-2.560.23361420.19972233X-RAY DIFFRACTION99
2.56-2.680.21961410.18492214X-RAY DIFFRACTION98.41
2.68-2.820.24151420.19432217X-RAY DIFFRACTION97.92
2.82-2.990.241410.19162217X-RAY DIFFRACTION97.6
2.99-3.220.2211410.1822208X-RAY DIFFRACTION97.39
3.22-3.550.22261410.18922209X-RAY DIFFRACTION96.79
3.55-4.060.17881400.17572179X-RAY DIFFRACTION95.16
4.06-5.120.24531390.17692179X-RAY DIFFRACTION93.66

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