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- PDB-2lbo: Eimeria tenella microneme protein 3 MAR_B domain -

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Basic information

Entry
Database: PDB / ID: 2lbo
TitleEimeria tenella microneme protein 3 MAR_B domain
ComponentsMicroneme protein 3
KeywordsCELL ADHESION / apicomplexan / eimeria tenella / protozoa / microneme / microneme adhesive repeat
Function / homologyActin; Chain A, domain 4 - #70 / Micronemal adhesive repeat, sialic-acid binding / Sialic-acid binding micronemal adhesive repeat / Actin; Chain A, domain 4 / Alpha-Beta Complex / Alpha Beta / Microneme protein 3
Function and homology information
Biological speciesEimeria tenella (eukaryote)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsLai, L. / Garnett, J. / Simpson, P. / Matthews, S.
CitationJournal: Plos Pathog. / Year: 2011
Title: The Role of Sialyl Glycan Recognition in Host Tissue Tropism of the Avian Parasite Eimeria tenella
Authors: Lai, L. / Bumstead, J. / Liu, Y. / Garnett, J. / Campanero-Rhodes, M.A. / Blake, D.P. / Palma, A.S. / Chai, W. / Ferguson, D.J. / Simpson, P. / Feizi, T. / Tomley, F.M. / Matthews, S.
History
DepositionApr 5, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microneme protein 3


Theoretical massNumber of molelcules
Total (without water)13,2991
Polymers13,2991
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Microneme protein 3


Mass: 13298.550 Da / Num. of mol.: 1 / Fragment: MAR_B DOMAIN, UNP residues 152-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eimeria tenella (eukaryote) / Gene: mic3 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami DE3 / References: UniProt: B6VCV4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: SOLUTION NMR STRUCTURE OF THE EIMERIA TENELLA MICRONEME PROTEIN 3 MAR_B DOMAIN
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CO)CA
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D HN(CO)CA
11023D 1H-13C NOESY
11113D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] EtMIC3_marb-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-98% 13C; U-98% 15N] EtMIC3_marb-4, 20 mM sodium phosphate-5, 50 mM sodium chloride-6, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMEtMIC3_marb-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMEtMIC3_marb-4[U-98% 13C; U-98% 15N]2
20 mMsodium phosphate-52
50 mMsodium chloride-62
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA2.2Linge, O'Donoghue and Nilgeschemical shift assignment
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
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: 10 / Representative conformer: 1

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