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- PDB-8b4s: Antimicrobial peptide capitellacin from polychaeta Capitella tele... -

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Basic information

Entry
Database: PDB / ID: 8b4s
TitleAntimicrobial peptide capitellacin from polychaeta Capitella teleta in DPC (dodecylphosphocholine) micelles, dimeric form
ComponentsBRICHOS domain-containing protein
KeywordsANTIMICROBIAL PROTEIN / PROTEIN / ANTIMICROBIAL PEPTIDE / BETA-HAIRPIN / DIMER
Function / homologyBRICHOS domain / BRICHOS domain profile. / membrane / BRICHOS domain-containing protein
Function and homology information
Biological speciesCapitella teleta (invertebrata)
MethodSOLUTION NMR / simulated annealing
AuthorsMironov, P.A. / Reznikova, O.V. / Paramonov, A.S. / Shenkarev, Z.O.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Education and Science of the Russian Federation075-15-2021-1049 Russian Federation
CitationJournal: Biomolecules / Year: 2024
Title: Dimerization of the beta-Hairpin Membrane-Active Cationic Antimicrobial Peptide Capitellacin from Marine Polychaeta: An NMR Structural and Thermodynamic Study.
Authors: Mironov, P.A. / Paramonov, A.S. / Reznikova, O.V. / Safronova, V.N. / Panteleev, P.V. / Bolosov, I.A. / Ovchinnikova, T.V. / Shenkarev, Z.O.
History
DepositionSep 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRICHOS domain-containing protein
B: BRICHOS domain-containing protein


Theoretical massNumber of molelcules
Total (without water)4,7782
Polymers4,7782
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area3740 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1target function

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Components

#1: Protein/peptide BRICHOS domain-containing protein


Mass: 2388.888 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capitella teleta (invertebrata) / Gene: CAPTEDRAFT_185237 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R7TSD6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic12D NOESY
121anisotropic12D 1H-1H TOCSY
131anisotropic12D 1H-13C HSQC aliphatic
141anisotropic12D 1H-13C HSQC aromatic
151anisotropic22D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle12 mg/mL capitellacin, 168 mM DPC, 5 % v/v [U-99% 2H] D2O, 95% H2O/5% D2Onatural_peptide95% H2O/5% D2O
micelle250 uM [U-100% 15N] capitellacin, 6.5 mM DPC, 5 % v/v [U-99% 2H] D2O, 95% H2O/5% D2O15N_peptide95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLcapitellacinnatural abundance1
168 mMDPCnatural abundance1
5 % v/vD2O[U-99% 2H]1
50 uMcapitellacin[U-100% 15N]2
6.5 mMDPCnatural abundance2
5 % v/vD2O[U-99% 2H]2
Sample conditionsDetails: The ratio of peptide:DPC is 1:100 / Ionic strength: 0.001 M / Label: 1 / pH: 5.4 / Pressure: AMBIENT Pa / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin3Bruker Biospincollection
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CARA1.9.1.7Keller and Wuthrichpeak picking
Refinement
MethodSoftware ordinal
simulated annealing2
simulated annealing1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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