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- PDB-2loe: Structure of the Plasmodium 6-cysteine s48/45 Domain -

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Basic information

Entry
Database: PDB / ID: 2loe
TitleStructure of the Plasmodium 6-cysteine s48/45 Domain
Components6-cysteine protein, putative
KeywordsMEMBRANE PROTEIN / Malaria
Function / homology
Function and homology information


symbiont-containing vacuolar space / symbiont entry into host / side of membrane / apical part of cell / cell surface / plasma membrane
Similarity search - Function
Immunoglobulin-like - #2860 / : / 6-Cysteine (6-Cys) domain / 6-Cysteine (6-Cys) domain superfamily / Sexual stage antigen s48/45 domain / 6-Cysteine (6-Cys) domain profile. / Sexual stage antigen s48/45 domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Merozoite surface protein P12 / Merozoite surface protein P12
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsCai, M. / Arredondo, S.A. / Clore, M.G. / Miller, L.H. / Takayama, Y. / Macdonald, N.J. / Enderson, E.D. / Aravind, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure of the Plasmodium 6-cysteine s48/45 domain.
Authors: Arredondo, S.A. / Cai, M. / Takayama, Y. / Macdonald, N.J. / Anderson, D.E. / Aravind, L. / Clore, G.M. / Miller, L.H.
History
DepositionJan 23, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Other
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Jun 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
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-cysteine protein, putative


Theoretical massNumber of molelcules
Total (without water)14,4101
Polymers14,4101
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 #1closest to the average

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Components

#1: Protein 6-cysteine protein, putative


Mass: 14410.165 Da / Num. of mol.: 1 / Fragment: UNP residues 174-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: Pf12, PFF0615c / Production host: Escherichia coli (E. coli) / References: UniProt: C6KSX0, UniProt: P19259*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution structure of the Plasmodium 6-cysteine s48/45 Domain
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1212D 1H-15N HSQC
1313D CBCA(CO)NH
1413D HBHA(CO)NH
1513D (H)CCH-TOCSY
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1812D 1H-13C HSQC
1912D 1H-13C HSQC aliphatic
11012D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 0.4 mM [U-99% 13C; U-99% 15N] Pf1 phage, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 0.4 mM / Component: Pf1 phage-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE9003

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Processing

NMR software
NameDeveloperClassification
PIPPGarrettchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1543
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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