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- PDB-2ln8: The solution structure of theromacin -

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Basic information

Entry
Database: PDB / ID: 2ln8
TitleThe solution structure of theromacin
ComponentsTheromacin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Defensin A-like - #100 / Macin / Macin superfamily / Macin / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHirudo medicinalis (medicinal leech)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsJung, S. / Soennichsen, F.D. / Hung, C.-W. / Tholey, A. / Boidin-Wichlacz, C. / Hausgen, W. / Gelhaus, C. / Desel, C. / Podschun, R. / Watzig, V. ...Jung, S. / Soennichsen, F.D. / Hung, C.-W. / Tholey, A. / Boidin-Wichlacz, C. / Hausgen, W. / Gelhaus, C. / Desel, C. / Podschun, R. / Watzig, V. / Tasiemski, A. / Leippe, M. / Groetzinger, J.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Macin family of antimicrobial proteins combines antimicrobial and nerve repair activities.
Authors: Jung, S. / Sonnichsen, F.D. / Hung, C.W. / Tholey, A. / Boidin-Wichlacz, C. / Haeusgen, W. / Gelhaus, C. / Desel, C. / Podschun, R. / Waetzig, V. / Tasiemski, A. / Leippe, M. / Grotzinger, J.
History
DepositionDec 20, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Aug 19, 2015Group: Structure summary
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / 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_spectrometer.model
Revision 1.4Oct 16, 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: Theromacin


Theoretical massNumber of molelcules
Total (without water)8,4661
Polymers8,4661
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 #1lowest energy

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Components

#1: Protein Theromacin


Mass: 8465.528 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Escherichia coli (E. coli) / References: UniProt: A8I0L8
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: The solution structure of Thermomacin
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1213D HNCA
1313D HNCO
1413D C(CO)NH
1513D H(CCO)NH
1613D HN(CO)CA
1713D HN(CA)CB
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY

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Sample preparation

DetailsContents: 1 mM [U-99% 13C; U-99% 15N] protein, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: entity-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 0.02 / pH: 7.4 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxstructure solution
NMRViewJohnson, One Moon Scientificprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificstructure solution
CYANAGuntert, Mumenthaler and Wuthrichprocessing
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readprocessing
CNSBrunger, Adams, Clore, Gros, Nilges and Readchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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