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- PDB-7osc: Solution structure of antimicrobial peptide cathelicidin-1 PcDode... -

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Basic information

Entry
Database: PDB / ID: 7osc
TitleSolution structure of antimicrobial peptide cathelicidin-1 PcDode from sperm whale Physeter catodon
Componentscathelicidin-1-like
KeywordsANTIMICROBIAL PROTEIN / CATHELICIDIN
Function / homologyCathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cathelicidin / Cystatin superfamily / defense response to bacterium / extracellular region / LOW QUALITY PROTEIN: cathelicidin-1-like
Function and homology information
Biological speciesPhyseter macrocephalus (sperm whale)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMironov, P.A. / Myshkin, M.Y. / 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
DepositionJun 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cathelicidin-1-like


Theoretical massNumber of molelcules
Total (without water)2,7881
Polymers2,7881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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 cathelicidin-1-like


Mass: 2787.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: LOC102973809 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Y9FJE4
Has ligand of interestN
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
121anisotropic12D 1H-1H NOESY
131anisotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.6 mM PCdode, 5 % [U-100% 2H] D2O, 95% H2O/5% D2O
Label: natural abundance / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMPCdodenatural abundance1
5 %D2O[U-100% 2H]1
Sample conditionsIonic strength: 0.01 mM / Label: condition_1 / pH: 4.4 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.13Guntert, Mumenthaler and Wuthrichrefinement
CARA1.9.1.7Keller and Wuthrichchemical shift assignment
CYANA3.98.13Guntert, Mumenthaler and Wuthrichstructure calculation
TopSpin4.0.7Bruker Biospincollection
CARA1.9.1.7Keller 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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