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- PDB-6cfa: peptide PaAMP1R3 -

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Basic information

Entry
Database: PDB / ID: 6cfa
Titlepeptide PaAMP1R3
Componentspeptide PaAMP1R3
KeywordsDE NOVO PROTEIN / design / helix
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsAlves, E.S.F. / Liao, L.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
FAPEG+556232018082 Brazil
CitationJournal: To be Published
Title: Synthetic peptide PaAMP1R3
Authors: Alves, E.S.F. / Liao, L.M.
History
DepositionFeb 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: peptide PaAMP1R3


Theoretical massNumber of molelcules
Total (without water)2,3051
Polymers2,3051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2150 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 peptide PaAMP1R3


Mass: 2305.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2 mM PaAMP1R3, 200 mM [U-98% 13C] DPC-d38, 10 % [U-99% 2H] D2O, 90 % H2O, 5 % 97% DSS, 90% H2O/10% D2O
Label: PaAMP1R3 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMPaAMP1R3natural abundance1
200 mMDPC-d38[U-98% 13C]1
10 %D2O[U-99% 2H]1
90 %H2Onatural abundance1
5 %DSS97%1
Sample conditionsIonic strength: sodium phosphate buffer mM / Ionic strength err: 1 / Label: paamp1r3 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: refinement in water
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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