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- PDB-2fcg: Solution structure of the C-terminal fragment of human LL-37 -

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Basic information

Entry
Database: PDB / ID: 2fcg
TitleSolution structure of the C-terminal fragment of human LL-37
ComponentsAntibacterial protein FALL-39, core peptideAntibiotic
KeywordsANTIMICROBIAL PROTEIN / LL-37 / host defense peptide / antimicrobial peptide
Function / homology
Function and homology information


cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection ...cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection / lipopolysaccharide binding / specific granule lumen / positive regulation of angiogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / cellular response to tumor necrosis factor / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cystatin superfamily
Similarity search - Domain/homology
Cathelicidin antimicrobial peptide
Similarity search - Component
MethodSOLUTION NMR / simulated annealing
AuthorsWang, G. / Li, X.
CitationJournal: J.Am.Chem.Soc. / Year: 2006
Title: Solution Structures of Human LL-37 Fragments and NMR-Based Identification of a Minimal Membrane-Targeting Antimicrobial and Anticancer Region.
Authors: Li, X. / Li, Y. / Han, H. / Miller, D.W. / Wang, G.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Antibacterial protein FALL-39, core peptide


Theoretical massNumber of molelcules
Total (without water)3,0511
Polymers3,0511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Antibacterial protein FALL-39, core peptide / Antibiotic / FALL-39 peptide antibiotic / Cationic antimicrobial protein CAP-18 / hCAP-18


Mass: 3050.623 Da / Num. of mol.: 1 / Fragment: residues 146-170 / Source method: obtained synthetically
Details: sequence corresponds to residues 146-170 of Human FALL-39
References: UniProt: P49913

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141(H1,H13) HSQC
151(H1,N15) HSQC
NMR detailsText: A set of NMR data was also collected at 310 K.

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Sample preparation

DetailsContents: 2 mM peptide and 80 mM SDS / Solvent system: 10% D2O/90%H2O
Sample conditionsIonic strength: 80 / pH: 5.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH1CD Schwieters, J Kuszewski, N Tjandra, GM Clorestructure solution
PIPP1Dan Garrettdata analysis
NMRPipe2.1Frank Delaglioprocessing
TALOS1999Cornilescu, Frank Delaglio, Ad Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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