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- PDB-2mwt: NMR structure of crotalicidin in DPC micelles -

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Basic information

Entry
Database: PDB / ID: 2mwt
TitleNMR structure of crotalicidin in DPC micelles
ComponentsCathelicidin-like peptide
Keywordsantimicrobial / antitumor protein / antimicrobial peptide / antitumor peptide / antimicrobial protein
Function / homology
Function and homology information


other organism cell membrane / defense response to fungus / lipopolysaccharide binding / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / extracellular space / membrane
Similarity search - Function
Cathelicidin-like / Cathelicidin / Cystatin superfamily
Similarity search - Domain/homology
Biological speciesCrotalus durissus terrificus (tropical rattlesnake)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model1
AuthorsJimenez, M. / Zamora-Carreras, H.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structural Dissection of Crotalicidin, a Rattlesnake Venom Cathelicidin, Retrieves a Fragment with Antimicrobial and Antitumor Activity.
Authors: Falcao, C.B. / Perez-Peinado, C. / de la Torre, B.G. / Mayol, X. / Zamora-Carreras, H. / Jimenez, M.A. / Radis-Baptista, G. / Andreu, D.
History
DepositionNov 24, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Cathelicidin-like peptide


Theoretical massNumber of molelcules
Total (without water)4,1671
Polymers4,1671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Cathelicidin-like peptide


Mass: 4167.423 Da / Num. of mol.: 1 / Fragment: residues 161-194 / Source method: obtained synthetically
Source: (synth.) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: U5KJM4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
2412D 1H-1H COSY
2512D 1H-1H TOCSY
2612D 1H-1H NOESY
1722D 1H-1H COSY
1822D 1H-1H TOCSY
1922D 1H-1H NOESY
11022D 1H-13C HSQC aliphatic
11122D 1H-13C HSQC aromatic
21222D 1H-1H COSY
21322D 1H-1H TOCSY
21422D 1H-1H NOESY
21522D 1H-13C HSQC aliphatic
21622D 1H-13C HSQC aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM crotalicidin, 30 mM [U-98% 2H] DPC, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM crotalicidin, 30 mM [U-98% 2H] DPC, 0.1 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcrotalicidin-11
30 mMDPC-2[U-98% 2H]1
0.1 mMDSS-31
1 mMcrotalicidin-42
30 mMDPC-5[U-98% 2H]2
0.1 mMDSS-62
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
103ambient 298 K
203ambient 308 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
SparkyGoddarddata analysis
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 461 / NOE intraresidue total count: 219 / NOE long range total count: 0 / NOE medium range total count: 116 / NOE sequential total count: 126 / Protein phi angle constraints total count: 30 / Protein psi angle constraints total count: 29
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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