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- PDB-2b9k: Solution structure of LCI, an AMP from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2b9k
TitleSolution structure of LCI, an AMP from Bacillus subtilis
ComponentsAntimicrobial peptide LCI
KeywordsANTIBIOTIC / BETA-STRANDED PROTEIN / AMP
Function / homology
Function and homology information


defense response to bacterium / extracellular region
Similarity search - Function
Anthopleurin-A - #70 / LCI fold / : / LCI fold / Anthopleurin-A / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Antimicrobial peptide LCI
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsXia, B. / Gong, W. / Lu, G.
CitationJournal: To be published
Title: Solution structure of LCI, an AMP from Bacillus subtilis
Authors: Xia, B. / Gong, W. / Lu, G.
History
DepositionOct 11, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 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
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antimicrobial peptide LCI


Theoretical massNumber of molelcules
Total (without water)5,4711
Polymers5,4711
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)21 / 100structures with lowest torsion angle energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Antimicrobial peptide LCI / AMP


Mass: 5471.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: A014 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETA / References: UniProt: P82243

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111DQF-COSY
121E-COSY
1312D TOCSY
1412D NOESY
152DQF-COSY
1622D TOCSY
1722D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM LCI; 50mM soldium acetate; 90% H2O, 10%D2O90% H2O/10% D2O
22mM LCI; 50mM soldium acetate; 100% D2O100% D2O
Sample conditionspH: 4.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
SANEBrendan M. Duggan, Glen B. Legge, H. Jane Dyson & Peter E. Wrightdata analysis
CYANA1.0.6Guntert, P., Mumenthaler, C., 'Wuthrich, K.structure solution
Amber7David A. Case, et.al.structure solution
Amber7David A. Case, et.al.refinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structures are based on a total of 1145 restraints, 1094 are NOE-derived distance constraints, 13 dihedral angle restraints, 38 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with lowest torsion angle energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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