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- PDB-2lud: Solution structure of a conformational mutant of the adhesion pro... -

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Basic information

Entry
Database: PDB / ID: 2lud
TitleSolution structure of a conformational mutant of the adhesion protein delta-Bd37 from Babesia divergens
ComponentsGlycosylphosphatidylinositol-anchored merozoite surface protein
KeywordsCELL INVASION / apicomplexa / babesia / erythrocyte binding protein / vaccine / Bd37
Function / homologyGlycosylphosphatidylinositol-anchored merozoite surface protein / Bd37, core domain superfamily / Glycosylphosphatidylinositol-anchored merozoite surface protein / host cell surface binding / side of membrane / vesicle / extracellular region / plasma membrane / Adhesion protein Bd37
Function and homology information
Biological speciesBabesia divergens (eukaryote)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
AuthorsMurciano, B. / Barthe, P. / Delbecq, S. / Roumestand, C.
Citation
Journal: To be Published
Title: Solution structure of a conformational mutant of the adhesion protein delta-Bd37 from Babesia divergens
Authors: Murciano, B. / Barthe, P. / Schetters, T. / Gorenflot, A. / Roumestand, C. / Delbecq, S.
#1: Journal: Biomol.Nmr Assign. / Year: 2013
Title: 1H, 15N and 13C Backbone resonance assignments of a conformational mutant of the adhesion protein delta-Bd37 from Babesia divergens.
Authors: Barthe, P. / Murciano, B. / Schetters, T. / Gorenflot, A. / Delbecq, S. / Roumestand, C.
History
DepositionJun 12, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Glycosylphosphatidylinositol-anchored merozoite surface protein


Theoretical massNumber of molelcules
Total (without water)24,5751
Polymers24,5751
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 / 600structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Glycosylphosphatidylinositol-anchored merozoite surface protein


Mass: 24575.314 Da / Num. of mol.: 1 / Mutation: K248A, E279A, D283A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Babesia divergens (eukaryote) / Gene: Bd37 / Plasmid: pIVEX 2.4.a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8T117

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-15N TOCSY
1323D HNCA
1423D CBCA(CO)NH
1523D HN(CA)CB
1623D HNCO
1723D HCACO
1823D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.45 mM [U-100% 15N] EDK-delta-Bd37, 90% H2O/10% D2O90% H2O/10% D2O
20.38 mM [U-100% 13C; U-100% 15N] EDK-delta-Bd37, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.45 mMEDK-delta-Bd37-1[U-100% 15N]1
0.38 mMEDK-delta-Bd37-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 50 / pH: 6.9 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
Gifa4.44Delsucprocessing
CINDY1.8Padilladata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1 / Details: RECOORD SCRIPTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 600 / Conformers submitted total number: 20

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