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- PDB-7acb: Covalent/noncovalent tetramer of Capra hircus Cathelicidin-1 in D... -

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Basic information

Entry
Database: PDB / ID: 7acb
TitleCovalent/noncovalent tetramer of Capra hircus Cathelicidin-1 in DPC (dodecylphosphocholine) micelles
ComponentsCapra hircus Cathelicidin-1 (dodecylphosphocholine)
KeywordsANTIMICROBIAL PROTEIN / PROTEIN
Biological speciesCapra hircus (goat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMyshkin, M.Y. / Mironov, P. / Shenkarev, Z.O.
CitationJournal: Front Microbiol / Year: 2021
Title: Dodecapeptide Cathelicidins of Cetartiodactyla: Structure, Mechanism of Antimicrobial Action, and Synergistic Interaction With Other Cathelicidins
Authors: Bolosov, I.A. / Panteleev, P.V. / Sychev, S.V. / Sukhanov, S.V. / Mironov, P.A. / Myshkin, M.Y. / Shenkarev, Z.O. / Ovchinnikova, T.V.
History
DepositionSep 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2Nov 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capra hircus Cathelicidin-1 (dodecylphosphocholine)
B: Capra hircus Cathelicidin-1 (dodecylphosphocholine)
C: Capra hircus Cathelicidin-1 (dodecylphosphocholine)
D: Capra hircus Cathelicidin-1 (dodecylphosphocholine)


Theoretical massNumber of molelcules
Total (without water)6,0364
Polymers6,0364
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Structure of ChDode dimer in DPC micelles was calculated based on the H-bonds and long range NOE contacts.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3340 Å2
ΔGint-32 kcal/mol
Surface area4760 Å2
MethodPISA
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
Capra hircus Cathelicidin-1 (dodecylphosphocholine)


Mass: 1508.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capra hircus (goat) / Production host: Escherichia coli (E. coli)
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
112isotropic32D 1H-1H NOESY
122isotropic32D 1H-1H TOCSY
131isotropic12D 1H-15N HSQC
151isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
micelle10.96 mM 15 Capra hircus Cathelicidin-1, 1.6 % [U-99% 2H] DPC, 95% H2O/5% D2OChDode 15N DPC95% H2O/5% D2O
micelle20.336 mM Capra hircus Cathelicidin-1 (dodecylphosphocholine), 1.6 % [U-99% 2H] DPC, 95% H2O/5% D2OChDode DPC95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.96 mMCapra hircus Cathelicidin-1151
1.6 %DPC[U-99% 2H]1
0.336 mMCapra hircus Cathelicidin-1 (dodecylphosphocholine)natural abundance2
1.6 %DPC[U-99% 2H]2
Sample conditionsIonic strength: 0.01 mM / Label: ChDode DPC / pH: 4 / Pressure: AMBIENT Pa / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III8001
Bruker AVANCE IIIBrukerAVANCE III6003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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