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- PDB-2jq2: NMR structure of the anticoccidial peptide PW2 in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2jq2
TitleNMR structure of the anticoccidial peptide PW2 in DPC micelles
Componentspw2
KeywordsANTIMICROBIAL PROTEIN / PW2 / DPC / membrane / antimicrobial
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
Model detailsPW2 structure in DPC micelles
AuthorsAlmeida, F.C. / Tinoco, L.W. / Gomes-Neto, F. / Valente, A.P.
Citation
Journal: J.Biomol.Nmr / Year: 2007
Title: Effect of micelle interface on the binding of anticoccidial PW2 peptide
Authors: Tinoco, L.W. / Gomes-Neto, F. / Valente, A.P. / Almeida, F.C.
#1: 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. / DaSilva Jr., A. / Leite, A. / Valente, A. / Almeida, F.C.L.
History
DepositionMay 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.5May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pw2


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_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide pw2


Mass: 1613.881 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was synthesized after being selected by phage display using Eimeria sp cells as a target.
Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: PW2 structure in DPC micelles
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY

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Sample preparation

DetailsContents: 2 mM pw2, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 2 mM / Component: pw2
Sample conditionsIonic strength: 0.1 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX4002

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Processing

NMR software
NameVersionDeveloperClassification
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSSOLVE1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 18

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