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- PDB-2lld: The Insect Defensin Lucifensin from Lucilia sericata -

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Basic information

Entry
Database: PDB / ID: 2lld
TitleThe Insect Defensin Lucifensin from Lucilia sericata
ComponentsLucifensin
KeywordsANTIMICROBIAL PROTEIN / maggot debridement therapy / antimicrobial peptide
Function / homology
Function and homology information


defense response to fungus / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / lipid binding / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Arthropod defensin / Invertebrate defensins family profile. / Defensin, invertebrate/fungal / Knottin, scorpion toxin-like superfamily
Similarity search - Domain/homology
Biological speciesLucilia sericata (common green bottle fly)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsNygaard, M.K.E. / Andersen, A.S. / Kristensen, H. / Krogfelt, K.A. / Fojan, P. / Wimmer, R.
CitationJournal: J.Biomol.Nmr / Year: 2012
Title: The insect defensin lucifensin from Lucilia sericata.
Authors: Nygaard, M.K. / Andersen, A.S. / Kristensen, H.H. / Krogfelt, K.A. / Fojan, P. / Wimmer, R.
History
DepositionNov 7, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lucifensin


Theoretical massNumber of molelcules
Total (without water)4,1301
Polymers4,1301
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 Lucifensin


Mass: 4129.804 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lucilia sericata (common green bottle fly)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P86471

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D DQF-COSY
1412D 1H-13C HSQC
1512D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 2 mM lucifensin, 10 mM potassium phosphate, 5 % D2O, 15 uM TSP, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMlucifensin-11
10 mMpotassium phosphate-21
5 %D2O-31
15 uMTSP-41
Sample conditionspH: 5.0 / Pressure: ambient / Temperature: 298.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
TALOS+Cornilescu, Delaglio and Baxgeometry optimization
YASARA11.5.21Elmar Kriegerrefinement
ProcheckNMRLaskowski and MacArthurstructure validation
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: First, in vacuo refinement with the NOVA force field, then refinement in explicit water with the YASARA force field
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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