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- PDB-2lu2: MIC5 regulates the activity of Toxoplasma subtilisin 1 by mimicki... -

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Basic information

Entry
Database: PDB / ID: 2lu2
TitleMIC5 regulates the activity of Toxoplasma subtilisin 1 by mimicking a subtilisin prodomain
ComponentsMicroneme TgMIC5 protein
KeywordsCELL ADHESION / Micronemal Protein 5 / invasion / pathogenesis
Function / homologyAlpha-Beta Plaits - #2380 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 2
AuthorsSaouros, S. / Dou, Z. / Henry, M. / Marchant, J. / Carruthers, V.B. / Matthews, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Microneme protein 5 regulates the activity of toxoplasma subtilisin 1 by mimicking a subtilisin prodomain.
Authors: Saouros, S. / Dou, Z. / Henry, M. / Marchant, J. / Carruthers, V.B. / Matthews, S.
History
DepositionJun 7, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microneme TgMIC5 protein


Theoretical massNumber of molelcules
Total (without water)15,2731
Polymers15,2731
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Microneme TgMIC5 protein / H4 / putative


Mass: 15272.904 Da / Num. of mol.: 1 / Fragment: UNP residues 98-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGME49_077080, TGVEG_027740 / Production host: Escherichia coli (E. coli) / References: UniProt: B6KRI2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 1H-15N NOESY
1913D 1H-13C NOESY
11013D HN(CA)CO
11113D (H)CC(CO)NH-TOCSY
11213D CCH-TOCSY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] Tg Micronemal Protein 5, 25 mM potassium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTg Micronemal Protein 5-1[U-100% 13C; U-100% 15N]1
25 mMpotassium phosphate-21
100 mMsodium chloride-31
Sample conditionsIonic strength: 0.1 / pH: 7.2 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker Avance IIBrukerAVANCE II8001
Bruker Avance IIIBrukerAVANCE III6002
Varian INOVAVarianINOVA9003

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxgeometry optimization
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonvalidation
TopSpinBruker Biospindata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: REFINED IN EXPLICIT WATER
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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