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- PDB-2k9b: Structure and membrane interactions of the antibiotic peptide der... -

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Basic information

Entry
Database: PDB / ID: 2k9b
TitleStructure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional solution and oriented 15N and 31P solid-state NMR spectroscopy
ComponentsDermadistinctin-K
KeywordsANTIBIOTIC / amphipathic alpha-helix / membrane protein structure determination / C-TERMINAL CARBOXYAMIDATION / ANTIMICROBIAL PROTEIN / Amphibian defense peptide / Antimicrobial / Secreted
Function / homologyDermaseptin / Dermaseptin / defense response to bacterium / extracellular region / Dermaseptin-DI1
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsMoraes, C.M. / Verly, R.M. / Resende, J.M. / Aisenbrey, C. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A. / Almeida, F.C.L. / Bechinger, B.
CitationJournal: Biophys.J. / Year: 2009
Title: Structure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional solution and oriented 15N and 31P solid-state NMR spectroscopy.
Authors: Verly, R.M. / de Moraes, C.M. / Resende, J.M. / Aisenbrey, C. / Bemquerer, M.P. / Pilo-Veloso, D. / Valente, A.P. / Almeida, F.C.L. / Bechinger, B.
History
DepositionOct 7, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

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Assembly

Deposited unit
A: Dermadistinctin-K


Theoretical massNumber of molelcules
Total (without water)3,1571
Polymers3,1571
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 / 500structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Dermadistinctin-K / DD K


Mass: 3156.699 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the peptide was prepared by solid-phase synthesis using Fmoc chemistry
References: UniProt: P83638
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of Dermadistinctin K (DD K) in DPC micelles
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY

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Sample preparation

DetailsContents: 2.0 mM dd k, 400 mM [U-2H] DPCd38, 400mM DPCd38/H2O
Solvent system: 400mM DPCd38/H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMdd k1
400 mMDPCd38[U-2H]1
Sample conditionspH: 6 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometerType: Bruker Avance III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
ProcheckNMRLaskowski and MacArthurdata analysis
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: NOE INTENSITIES WERE CONVERTED INTO SEMI-QUANTITATIVE DISTANCE RESTRAINS. THE UPPER LIMITS OF THE DISTANCES RESTRAINS THUS OBTAINED WERE 2.8, 3.4 AND 5.0 A (STRONG, MEDIUM, AND WEAK NOES ...Details: NOE INTENSITIES WERE CONVERTED INTO SEMI-QUANTITATIVE DISTANCE RESTRAINS. THE UPPER LIMITS OF THE DISTANCES RESTRAINS THUS OBTAINED WERE 2.8, 3.4 AND 5.0 A (STRONG, MEDIUM, AND WEAK NOES RESPECTIVELY). STRUCTURE CALCULATIONS WERE PERFORMED USING THE XPLOR-NIH SOFTWARE, VERSION 2.17.0 (SCHWIETERS ET AL., 2003). STARTING WITH THE EXTENDED STRUCTURE, 500 STRUCTURES WERE GENERATED USING A SIMULATED ANNEALING PROTOCOL. THIS WAS FOLLOWED BY 20000 STEPS OF SIMULATED ANNEALING AT 1000 K AND A SUBSEQUENT DECREASE IN TEMPERATURE IN 15000 STEPS IN THE FIRST SLOW-COOL ANNEALING STAGE.
NMR constraintsNOE constraints total: 270 / NOE intraresidue total count: 169 / NOE medium range total count: 31 / NOE sequential total count: 70
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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