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- PDB-4a5v: Solution structure ensemble of the two N-terminal apple domains (... -

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Basic information

Entry
Database: PDB / ID: 4a5v
TitleSolution structure ensemble of the two N-terminal apple domains (residues 58-231) of Toxoplasma gondii microneme protein 4
ComponentsMICRONEMAL PROTEIN 4
KeywordsADHESION
Function / homology
Function and homology information


microneme / cytoplasmic vesicle / cell adhesion / proteolysis / extracellular region
Similarity search - Function
PAN domain / divergent subfamily of APPLE domains / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain
Similarity search - Domain/homology
Micronemal protein 4
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodSOLUTION NMR / ARIA
AuthorsMarchant, J. / Cowper, B. / Liu, Y. / Lai, L. / Pinzan, C. / Marq, J.B. / Friedrich, N. / Sawmynaden, K. / Chai, W. / Childs, R.A. ...Marchant, J. / Cowper, B. / Liu, Y. / Lai, L. / Pinzan, C. / Marq, J.B. / Friedrich, N. / Sawmynaden, K. / Chai, W. / Childs, R.A. / Saouros, S. / Simpson, P. / Barreira, M.C.R. / Feizi, T. / Soldati-Favre, D. / Matthews, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Galactose Recognition by the Apicomplexan Parasite Toxoplasma Gondii.
Authors: Marchant, J. / Cowper, B. / Liu, Y. / Lai, L. / Pinzan, C. / Marq, J.B. / Friedrich, N. / Sawmynaden, K. / Liew, L. / Chai, W. / Childs, R.A. / Saouros, S. / Simpson, P. / Roque Barreira, M. ...Authors: Marchant, J. / Cowper, B. / Liu, Y. / Lai, L. / Pinzan, C. / Marq, J.B. / Friedrich, N. / Sawmynaden, K. / Liew, L. / Chai, W. / Childs, R.A. / Saouros, S. / Simpson, P. / Roque Barreira, M.C. / Feizi, T. / Soldati-Favre, D. / Matthews, S.
History
DepositionOct 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Jun 23, 2021Group: Data collection / Other
Category: pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr ..._pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.field_strength
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MICRONEMAL PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)17,2431
Polymers17,2431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein MICRONEMAL PROTEIN 4 / MIC4


Mass: 17243.074 Da / Num. of mol.: 1 / Fragment: APPLE DOMAINS 1 AND 2, RESIDUES 58-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: PET32 XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XZH7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCA(CO)NH
221HN(CA)CB
331HNCO
441HN(CA)CO
551(H)CC(CO)NH-TOCSY
661H(C) CH-TOCSY
771(H)CCH-TOCSY
881C-NOESY- HSQC
991N-NOESY- HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED MIC4 APPLE DOMAINS 1 AND 2

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Sample preparation

Details
Solution-IDContents
190 % WATER / 10 % D2O
2100 % D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM6.5 1.0 atm303.0 K
2100 mM6.5 1.0 atm303.0 K
3100 mM6.5 1.0 atm303.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Varian8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-refinement
NMRViewstructure solution
TALOSstructure solution
ARIAstructure solution
CNSstructure solution
RefinementMethod: ARIA / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 10

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