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- PDB-2lre: The solution structure of the dimeric Acanthaporin -

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Basic information

Entry
Database: PDB / ID: 2lre
TitleThe solution structure of the dimeric Acanthaporin
ComponentsAcanthaporin
KeywordsANTIMICROBIAL PROTEIN / Pore-forming toxin / alpha helix
Function / homologyArc Repressor Mutant, subunit A - #1840 / : / Acanthaporin / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / identical protein binding / Acanthaporin
Function and homology information
Biological speciesAcanthamoeba culbertsoni (eukaryote)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model
AuthorsMichalek, M. / Soennichsen, F.D. / Wechselberger, R. / Dingley, A.J. / Wienk, H. / Simanski, M. / Herbst, R. / Lorenzen, I. / Marciano-Cabral, F. / Gelhaus, C. ...Michalek, M. / Soennichsen, F.D. / Wechselberger, R. / Dingley, A.J. / Wienk, H. / Simanski, M. / Herbst, R. / Lorenzen, I. / Marciano-Cabral, F. / Gelhaus, C. / Groetzinger, J. / Leippe, M.
CitationJournal: Nat.Chem.Biol. / Year: 2013
Title: Structure and function of a unique pore-forming protein from a pathogenic acanthamoeba.
Authors: Michalek, M. / Sonnichsen, F.D. / Wechselberger, R. / Dingley, A.J. / Hung, C.W. / Kopp, A. / Wienk, H. / Simanski, M. / Herbst, R. / Lorenzen, I. / Marciano-Cabral, F. / Gelhaus, C. / ...Authors: Michalek, M. / Sonnichsen, F.D. / Wechselberger, R. / Dingley, A.J. / Hung, C.W. / Kopp, A. / Wienk, H. / Simanski, M. / Herbst, R. / Lorenzen, I. / Marciano-Cabral, F. / Gelhaus, C. / Gutsmann, T. / Tholey, A. / Grotzinger, J. / Leippe, M.
History
DepositionMar 28, 2012Deposition site: BMRB / Processing site: RCSB
SupersessionMay 2, 2012ID: 2KUJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 26, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acanthaporin
B: Acanthaporin


Theoretical massNumber of molelcules
Total (without water)12,0022
Polymers12,0022
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)17 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Acanthaporin


Mass: 6001.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba culbertsoni (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: I3NI56*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-1H TOCSY
1322D 1H-1H NOESY
1413D 1H-15N NOESY
1513D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-100% 15N] acanthaporin_dimer, 25 mM [U-2H] TRIS, 0.001 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
20.7 mM [U-100% 15N] acanthaporin_dimer, 25 mM [U-2H] TRIS, 0.001 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMacanthaporin_dimer-1[U-100% 15N]1
25 mMTRIS-2[U-2H]1
0.001 %sodium azide-31
0.7 mMacanthaporin_dimer-4[U-100% 15N]2
25 mMTRIS-5[U-2H]2
0.001 %sodium azide-62
Sample conditionsIonic strength: 0.025 / pH: 8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7502

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 17

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