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- PDB-2mgr: Structure of Plasmodium Yoelii Merozoite Surface Protein 1 - C-te... -

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Basic information

Entry
Database: PDB / ID: 2mgr
TitleStructure of Plasmodium Yoelii Merozoite Surface Protein 1 - C-terminal Domain, E28K mutant
ComponentsMerozoite surface protein 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


side of membrane / extracellular region / plasma membrane
Similarity search - Function
Merozoite surface 1, C-terminal / Merozoite surface protein, EGF domain 1 / Merozoite surface protein 1 (MSP1) C-terminus / MSP1 EGF domain 1 / Laminin / Laminin / Ribbon / Mainly Beta
Similarity search - Domain/homology
Merozoite surface protein 1
Similarity search - Component
Biological speciesPlasmodium yoelii yoelii (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsCurd, R.D. / Birdsall, B. / Kadekoppala, M. / Ogun, S. / Kelly, G. / Holder, A.A.
CitationJournal: OPEN BIOLOGY / Year: 2014
Title: The structure of Plasmodium yoelii merozoite surface protein 119, antibody specificity and implications for malaria vaccine design
Authors: Curd, R.D. / Birdsall, B. / Kadekoppala, M. / Ogun, S.A. / Kelly, G. / Holder, A.A.
History
DepositionNov 4, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Merozoite surface protein 1


Theoretical massNumber of molelcules
Total (without water)10,7301
Polymers10,7301
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Merozoite surface protein 1


Mass: 10729.788 Da / Num. of mol.: 1 / Fragment: C-terminal Domain, UNP residues 1656-1754 / Mutation: N25D, E28K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium yoelii yoelii (eukaryote) / Gene: MSP-1 / Production host: Komagataella pastoris (fungus) / References: UniProt: P13828

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D H(CCO)NH
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1912D 1H-13C HSQC

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] MSP1_19-1, 25 mM potassium phosphate-2, 50 mM potassium chloride-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMSP1_19-1[U-99% 13C; U-99% 15N]1
25 mMpotassium phosphate-21
50 mMpotassium chloride-31
Sample conditionsIonic strength: 75 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE6003
Varian INOVAVarianINOVA6004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe7.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddardchemical shift assignment
Sparky3Goddarddata analysis
ARIA/CNS2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA/CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Standard SA protocol using ARIA with final water refinement
NMR constraintsNOE constraints total: 2004 / NOE intraresidue total count: 845 / NOE long range total count: 667 / NOE medium range total count: 179 / NOE sequential total count: 457 / Hydrogen bond constraints total count: 12 / Protein phi angle constraints total count: 53 / Protein psi angle constraints total count: 53
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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