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- PDB-2k35: Hydramacin-1: Structure and antibacterial activity of a peptide f... -

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Basic information

Entry
Database: PDB / ID: 2k35
TitleHydramacin-1: Structure and antibacterial activity of a peptide from the basal metazoan Hydra
Componentshydramacin-1
KeywordsANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


other organism cell membrane / defense response to bacterium / innate immune response / extracellular region / membrane
Similarity search - Function
Defensin A-like - #100 / Macin / Macin superfamily / Macin / Defensin A-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHydra (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsJung, S. / Dingley, A.J. / Stanisak, M. / Gelhaus, C. / Bosch, T. / Podschun, R. / Leippe, M. / Gr tzinger, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Hydramacin-1, structure and antibacterial activity of a protein from the Basal metazoan hydra.
Authors: Jung, S. / Dingley, A.J. / Augustin, R. / Anton-Erxleben, F. / Stanisak, M. / Gelhaus, C. / Gutsmann, T. / Hammer, M.U. / Podschun, R. / Bonvin, A.M. / Leippe, M. / Bosch, T.C. / Grotzinger, J.
History
DepositionApr 22, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hydramacin-1


Theoretical massNumber of molelcules
Total (without water)7,0291
Polymers7,0291
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)25 / 500target function
RepresentativeModel #1fewest violations

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Components

#1: Protein hydramacin-1


Mass: 7029.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydra (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: B3RFR8*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HNCO
1313D H(CCO)NH
1413D C(CO)NH
1513D HCACO
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D 1H-13C NOESY
11113D (H)CCH-TOCSY

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Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] hydramacin-1, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 1.0 mM / Component: hydramacin-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.050 / pH: 5.7 / Pressure: ambient / Temperature: 298 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
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: HADDOCK SOFTWARE INCLUDING A WATER SHELL IS ALSO USED FOR REFINEMENT
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 25

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