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- PDB-6d2h: Three-Dimensional Structures of [Phe3]Cm-p1 analogs -

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Basic information

Entry
Database: PDB / ID: 6d2h
TitleThree-Dimensional Structures of [Phe3]Cm-p1 analogs
ComponentsSER-ARG-PHE-GLU-LEU-ILE-VAL-HIS-GLN-ARG-NH2
KeywordsANTIFUNGAL PROTEIN / SDS micelles / antifungal peptide
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / simulated annealing
AuthorsAlves, E.S.F. / Liao, L.M.
Funding support Brazil, 1items
OrganizationGrant numberCountry
CNPq#55613211-9000 Brazil
CitationJournal: To be Published
Title: Three-Dimensional Structures of Cm-p1 and [Phe 3]Cm-p1 analogs
Authors: Alves, E.S.F. / Carvalho, O.R. / Franco, O.L. / Freitas, s.M. / Oliveira, A.L. / Verly, R.M. / Liao, L.M.
History
DepositionApr 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SER-ARG-PHE-GLU-LEU-ILE-VAL-HIS-GLN-ARG-NH2


Theoretical massNumber of molelcules
Total (without water)1,2851
Polymers1,2851
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 area1250 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 SER-ARG-PHE-GLU-LEU-ILE-VAL-HIS-GLN-ARG-NH2


Mass: 1285.498 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

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Sample preparation

DetailsType: solution
Contents: 1 mM cm-p1_analogous, 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: cm-p1_analogous / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcm-p1_analogousnatural 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: cm-p1_analogous / pH: 4 / 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-PLORBrungerstructure 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: 2
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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