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- PDB-1m02: NMR Structure of PW2 Bound to SDS Micelles: A Tryptophan-rich Ant... -

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Basic information

Entry
Database: PDB / ID: 1m02
TitleNMR Structure of PW2 Bound to SDS Micelles: A Tryptophan-rich Anticocidial Peptide Selected from Phage Display Libraries
ComponentsHIS-PRO-LEU-LYS-GLN-TYR-TRP-TRP-ARG-PRO-SER-ILE
KeywordsDE NOVO PROTEIN / Anticoccidial peptide / Eimeria / SDS / micelle / antimicrobial / pw2
MethodSOLUTION NMR / simulated annealing
AuthorsTinoco, L.W. / da Silva Jr., A. / Leite, A. / Valente, A.P. / Almeida, F.C.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: NMR structure of PW2 bound to SDS micelles. A tryptophan-rich anticoccidial peptide selected from phage display libraries
Authors: Tinoco, L.W. / Da Silva Jr., A. / Leite, A. / Valente, A.P. / Almeida, F.C.
#1: Journal: MOL.BIOCHEM.PARASITOL. / Year: 2002
Title: Avian anticoccidial activity of a novel membrane-interactive peptide selected from phage display libraries
Authors: da Silva Jr., A. / Kawazoe, U. / Freitas, F.F. / Gatti, M.S. / Dolder, H. / Schumacher, R.I. / Juliano, M.A. / da Silva, M.J. / Leite, A.
History
DepositionJun 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 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: HIS-PRO-LEU-LYS-GLN-TYR-TRP-TRP-ARG-PRO-SER-ILE


Theoretical massNumber of molelcules
Total (without water)1,6141
Polymers1,6141
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide HIS-PRO-LEU-LYS-GLN-TYR-TRP-TRP-ARG-PRO-SER-ILE / PW2


Mass: 1613.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: solid phase synthesis

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY

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Sample preparation

DetailsContents: 4 mM PW2
Solvent system: 20 mM sodium phosphate buffer, 160 mM SDS-d25, 10% D20
Sample conditionsIonic strength: 100 mM sodium chloride / pH: 5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX4002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, F. Grzesiek, S., Zhu, G., Vuister, G. W., Pfeifer, J. and Bax, A.processing
NMRView4.1.2Johnson, B. A. and Blevins, R. A.data analysis
CNS1.1Brunger, A. T., Adams, P.D., Clore, G.M., Delano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: cartesian dynamics
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 19

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