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- PDB-6mi9: The peptide PaAMP1B3 is an analog derived from the PaAMP1. The se... -

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Entry
Database: PDB / ID: 6mi9
TitleThe peptide PaAMP1B3 is an analog derived from the PaAMP1. The sequence of the ribosomal protein of Pyrobaculum aerophylum was used as template for rational design, using the Joker algorithm.
ComponentsPRO-MET-ALA-ARG-ASN-LYS-ILE-LEU-GLY-LYS-ILE-LEU-ARG-LYS-ILE-ALA-ALA-PHE-LYS
KeywordsANTIMICROBIAL PROTEIN / PAM
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsMundim, H.M. / Alves, E.S.F. / Rodrigues, L.V. / Liao, L.M.
CitationJournal: To Be Published
Title: NMR SOLUTION STRUCTURE OF THE ANTIMICROBIAL PEPTIDE PAAMP1B3.
Authors: Mundim, H.M. / Alves, E.S.F. / Liao, L.M.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: PRO-MET-ALA-ARG-ASN-LYS-ILE-LEU-GLY-LYS-ILE-LEU-ARG-LYS-ILE-ALA-ALA-PHE-LYS


Theoretical massNumber of molelcules
Total (without water)2,1731
Polymers2,1731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2120 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PRO-MET-ALA-ARG-ASN-LYS-ILE-LEU-GLY-LYS-ILE-LEU-ARG-LYS-ILE-ALA-ALA-PHE-LYS


Mass: 2172.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-13C HSQC
141isotropic12D 1H-15N HMQC

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Sample preparation

DetailsType: solution
Contents: 1 mM PaAMP1B3, 100 mM [U-98% 2H] SDS-D25, 5 % v/v [U-98% 2H] TMSP-d4, 90 % v/v H2O, 10 % v/v [U-99% 2H] D2O, 90% H2O/10% D2O
Label: PaAMP1B3 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMPaAMP1B3natural abundance1
100 mMSDS-D25[U-98% 2H]1
5 % v/vTMSP-d4[U-98% 2H]1
90 % v/vH2Onatural abundance1
10 % v/vD2O[U-99% 2H]1
Sample conditionsIonic strength: acid Not defined / Label: PaAMP1B3 / pH: 4.3 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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