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- PDB-1d6x: THE STRUCTURE OF THE ANTIMICROBIAL PEPTIDE TRITRPTICIN BOUND TO M... -

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Basic information

Entry
Database: PDB / ID: 1d6x
TitleTHE STRUCTURE OF THE ANTIMICROBIAL PEPTIDE TRITRPTICIN BOUND TO MICELLES-A DISTINCT MEMBRANE-BOUND PEPTIDE FOLD
ComponentsANTIMICROBIAL PEPTIDE, TRITRPTICIN
KeywordsIMMUNE SYSTEM / TYPE IV TURN-TYPE III TURN
MethodSOLUTION NMR / RESTRAINED SIMULATED ANNEALING, MOLECULAR DYNAMICS
Model type detailsminimized average
AuthorsSchibli, D.J. / Hwang, P.M. / Vogel, H.J.
Citation
Journal: Biochemistry / Year: 1999
Title: Structure of the antimicrobial peptide tritrpticin bound to micelles: a distinct membrane-bound peptide fold.
Authors: Schibli, D.J. / Hwang, P.M. / Vogel, H.J.
#1: Journal: FEBS Lett. / Year: 1996
Title: Antimicrobial Activity of a 13 Amino Acid Tryptophan-Rich Peptide Derived From a Putative Porcine Precursor Protein of a Novel Family of Antibacterial Peptides
Authors: Lawyer, C. / Pai, S. / Watabe, M. / Borgia, P. / Mashimo, T. / Eagleton, L. / Watabe, K.
History
DepositionOct 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTIMICROBIAL PEPTIDE, TRITRPTICIN


Theoretical massNumber of molelcules
Total (without water)1,9061
Polymers1,9061
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)19 / 97structures with favorable non-bond energy
RepresentativeModel #19minimized average structure

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Components

#1: Protein/peptide ANTIMICROBIAL PEPTIDE, TRITRPTICIN


Mass: 1906.286 Da / Num. of mol.: 1 / Fragment: SYNTHETIC CATHELICIDIN FRAGMENT / Source method: obtained synthetically
Details: SYNTHETIC PEPTIDE, SEQUENCE FROM A FRAGMENT OF A PORCINE NEUTROPHIL CATHELICIDIN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY
1422D NOESY
152TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES

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Sample preparation

Details
Solution-IDContents
13 MM TRITRPTICIN, 400 MM PERDEUTERATED SDS
23 MM TRITRPTICIN, 400 MM PERDEUTERATED SDS
Sample conditionsIonic strength: 400 mM SDS / pH: 4.5 / Pressure: AMBIENT / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe5DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER, BAXprocessing
CNS0.9BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
RefinementMethod: RESTRAINED SIMULATED ANNEALING, MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON 163 INTERPROTON RESTRAINTS. OF THESE 47 WERE INTRARESIDUE, 50 SEQUENTIAL, AND 66 SHORT-RANGE
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 97 / Conformers submitted total number: 19

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