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- PDB-6tj3: P. falciparum essential light chain, N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6tj3
TitleP. falciparum essential light chain, N-terminal domain
ComponentsPfELC
KeywordsMOTOR PROTEIN / motility / glideosome / light chain / myosin
Function / homologyEF-hand domain pair / Myosin essential light chain ELC
Function and homology information
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodSOLUTION NMR / simulated annealing
AuthorsWeininger, U. / Pazicky, S. / Loew, C.
Funding support Germany, Sweden, 2items
OrganizationGrant numberCountry
Joachim Herz Foundation800026 Germany
Swedish Research Council621-2013-5905 Sweden
CitationJournal: Commun Biol / Year: 2020
Title: Structural role of essential light chains in the apicomplexan glideosome.
Authors: Pazicky, S. / Dhamotharan, K. / Kaszuba, K. / Mertens, H.D.T. / Gilberger, T. / Svergun, D. / Kosinski, J. / Weininger, U. / Low, C.
History
DepositionNov 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PfELC


Theoretical massNumber of molelcules
Total (without water)8,9341
Polymers8,9341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, Protein is a monomer in solution.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5090 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein PfELC


Mass: 8934.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1017500 / Plasmid: pNIC28_Bsa4 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8IJM4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
142isotropic12D 1H-13C HSQC aromatic
153isotropic12D 1H-13C HSQC aromatic
161isotropic13D HN(CA)CB
171isotropic13D HN(COCA)CB
191isotropic23D H(CCO)NH
181isotropic23D H(CCO)NH
1101isotropic13D (H)CCH-TOCSY
1111isotropic12D (HB)CB(CGCD)HD
1121isotropic12D (H)CCH-TOCSY aromatic
1131isotropic13D 1H-15N NOESY
1151isotropic13D 1H-13C NOESY aliphatic
1142isotropic13D 1H-13C NOESY aromatic
1163isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.0 mM [U-99% 13C; U-99% 15N] ELC 1-74, 90% H2O/10% D2O15N13C sample90% H2O/10% D2O
solution21.0 mM 1-13C1 glucose ELC 1-74, 90% H2O/10% D2O1-13C sample90% H2O/10% D2O
solution31.0 mM 2-13C1 glucose ELC 1-74, 90% H2O/10% D2O2-13C samples90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMELC 1-74[U-99% 13C; U-99% 15N]1
1.0 mMELC 1-741-13C1 glucose2
1.0 mMELC 1-742-13C1 glucose3
Sample conditionsDetails: 50 mM HEPES, 20mM NaCl, 0.5mM TCEP / Ionic strength: 70 mM / Ionic strength err: 1 / Label: conditions 1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 bar / Temperature: 288 K / Temperature err: 0.5

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8001
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
ARIALinge, O'Donoghue and Nilgesstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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