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- PDB-2lt8: Eurocin solution structure -

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Basic information

Entry
Database: PDB / ID: 2lt8
TitleEurocin solution structure
Componentseurocin
KeywordsANTIMICROBIAL PROTEIN / a/b-fold / Cysteine stabilised
Function / homology
Function and homology information


protein-lipid complex / other organism cell membrane / immune system process / defense response to Gram-positive bacterium / lipid binding / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Arthropod defensin / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like / Knottin, scorpion toxin-like superfamily / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Fungal defensin eurocin
Similarity search - Component
Biological speciesEurotium amstelodami (mold)
MethodSOLUTION NMR / simulated annealing
AuthorsOeemig, J.S. / Lynggaard, C. / Knudsen, D.H. / Hansen, F.T. / Noergaard, K.D. / Schneider, T. / Vad, B.S. / Neve, S. / Kristensen, H. / Sahl, H. ...Oeemig, J.S. / Lynggaard, C. / Knudsen, D.H. / Hansen, F.T. / Noergaard, K.D. / Schneider, T. / Vad, B.S. / Neve, S. / Kristensen, H. / Sahl, H. / Otzen, D.E. / Wimmer, R.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Eurocin, a New Fungal Defensin: STRUCTURE, LIPID BINDING, AND ITS MODE OF ACTION.
Authors: Oeemig, J.S. / Lynggaard, C. / Knudsen, D.H. / Hansen, F.T. / Norgaard, K.D. / Schneider, T. / Vad, B.S. / Sandvang, D.H. / Nielsen, L.A. / Neve, S. / Kristensen, H.H. / Sahl, H.G. / Otzen, D.E. / Wimmer, R.
History
DepositionMay 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eurocin


Theoretical massNumber of molelcules
Total (without water)4,3491
Polymers4,3491
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/peptide eurocin


Mass: 4348.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eurotium amstelodami (mold) / Production host: Aspergillus oryzae (mold) / References: UniProt: K7N5L0*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
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1412D 1H-1H TOCSY
1512D DQF-COSY
1612D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.68 mM eurocin, 95 mM formic acid, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
1.68 mMeurocin-11
95 mMformic acid-21
Sample conditionspH: 4.5 / Pressure: ambient / Temperature: 298.1 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
XEASY1.5.5Bartels et al.chemical shift assignment
TopSpin1.3Bruker Biospincollection
YASARA12.1.19Dr. Elmar Kriegerrefinement
ProcheckNMRLaskowski and MacArthurstructure validation
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 276 / NOE intraresidue total count: 97 / NOE long range total count: 56 / NOE medium range total count: 39 / NOE sequential total count: 84 / Protein phi angle constraints total count: 16 / Protein psi angle constraints total count: 17
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 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.08 Å

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