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- PDB-2mbd: Lasiocepsin -

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Basic information

Entry
Database: PDB / ID: 2mbd
TitleLasiocepsin
Componentslasiocepsin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial peptide / wild bee / venom
Function / homologyLasiocepsin
Function and homology information
Biological speciesLasioglossum laticeps (insect)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, simulated annealing
Model detailsclosest to the average, model1
AuthorsMonincova, L. / Budesinsky, M. / Cujova, S. / Cerovsky, V. / Veverka, V.
CitationJournal: Chembiochem / Year: 2014
Title: Structural basis for antimicrobial activity of lasiocepsin.
Authors: Monincova, L. / Budesinsky, M. / Cujova, S. / Cerovsky, V. / Veverka, V.
History
DepositionJul 30, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: lasiocepsin


Theoretical massNumber of molelcules
Total (without water)2,9071
Polymers2,9071
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)48 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide lasiocepsin


Mass: 2906.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lasioglossum laticeps (insect) / References: UniProt: W5IDB3*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D 1H-15N HSQC
1412D 1H-13C HSQC

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Sample preparation

DetailsContents: 4 mM lasiocepsin, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 4 mM / Component: lasiocepsin-1
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 298 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
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
SPARKYGoddarddata analysis
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, simulated annealing
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 48

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