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- PDB-1ut3: Solution Structure of Spheniscin-2, a beta-Defensin from Penguin ... -

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Basic information

Entry
Database: PDB / ID: 1ut3
TitleSolution Structure of Spheniscin-2, a beta-Defensin from Penguin Stomach Preserving Food
ComponentsSPHENISCIN-2
KeywordsANTIBIOTIC / ANTIMICROBIAL PEPTIDE / PENGUIN / DEFENSIN / GASTROINTESTINAL IMMUNITY / FUNGICIDE
Function / homologyBeta defensin type / Beta defensin / defense response to fungus / killing of cells of another organism / defense response to bacterium / extracellular region / Spheniscin-2
Function and homology information
Biological speciesAPTENODYTES PATAGONICUS (king penguin)
MethodSOLUTION NMR
AuthorsLandon, C. / Labbe, H. / Thouzeau, C. / Bulet, P. / Vovelle, F.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Solution Structure of Spheniscin, a {Beta}-Defensin from the Penguin Stomach
Authors: Landon, C. / Thouzeau, C. / Labbe, H. / Bulet, P. / Vovelle, F.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Spheniscins, Avian Beta-Defensins in Preserved Stomach Contents of the King Penguin, Aptenodytes Patagonicus.
Authors: Thouzeau, C. / Le Maho, Y. / Froget, G. / Sabatier, L. / Le Bohec, C. / Hoffmann, J.A. / Bulet, P.
History
DepositionDec 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 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 / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPHENISCIN-2


Theoretical massNumber of molelcules
Total (without water)4,5171
Polymers4,5171
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 / 100LOWEST ENERGY, LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein/peptide SPHENISCIN-2 / SPHE-2 / PBD-2


Mass: 4517.485 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE STUDIES ON THE KING PENGUINS WERE CARRIED OUT ON POSSESSION ISLAND, CROZET ARCHIPELAGO.
Source: (synth.) APTENODYTES PATAGONICUS (king penguin) / References: UniProt: P83430
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-1H-COSY
1212D-1H-TOCSY
1312D-1H-NOESY

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Sample preparation

Sample conditionspH: 4.3 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
ARIA1.1/CNS1.1LINGErefinement
ARIA/CNSstructure solution
NMR ensembleConformer selection criteria: LOWEST ENERGY, LEAST RESTRAINT VIOLATION
Conformers calculated total number: 100 / Conformers submitted total number: 10

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