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- PDB-1cw6: REFINED SOLUTION STRUCTURE OF LEUCOCIN A -

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Basic information

Entry
Database: PDB / ID: 1cw6
TitleREFINED SOLUTION STRUCTURE OF LEUCOCIN A
ComponentsTYPE IIA BACTERIOCIN LEUCOCIN A
KeywordsTOXIN / ANTIMICROBIAL PEPTIDE / BACTERIOCIN
Function / homologyBacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Bacteriocin class IIa domain superfamily / Class II bacteriocin / Bacteriocin class IIa family signature. / killing of cells of another organism / defense response to bacterium / extracellular region / Bacteriocin leucocin-A
Function and homology information
Biological speciesLeuconostoc gelidum (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWang, Y. / Henz, M.E. / Gallagher, N.L.F. / Chai, S. / Yan, L.Z. / Gibbs, A.C. / Stiles, M.E. / Wishart, D.S. / Vederas, J.C.
CitationJournal: Biochemistry / Year: 1999
Title: Solution structure of carnobacteriocin B2 and implications for structure-activity relationships among type IIa bacteriocins from lactic acid bacteria.
Authors: Wang, Y. / Henz, M.E. / Gallagher, N.L. / Chai, S. / Gibbs, A.C. / Yan, L.Z. / Stiles, M.E. / Wishart, D.S. / Vederas, J.C.
History
DepositionAug 25, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TYPE IIA BACTERIOCIN LEUCOCIN A


Theoretical massNumber of molelcules
Total (without water)3,9371
Polymers3,9371
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)18 / 18STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #9closest to the average

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Components

#1: Protein/peptide TYPE IIA BACTERIOCIN LEUCOCIN A


Mass: 3937.323 Da / Num. of mol.: 1 / Fragment: LEUCOCIN A-UAL 187 / Source method: isolated from a natural source / Source: (natural) Leuconostoc gelidum (bacteria) / References: UniProt: P34034
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D NOESY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES. THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

DetailsContents: 2MM LEUCOCIN A IN 90% TFE-D3,10% H2O
Sample conditionsIonic strength: 0 / pH: 2.8 / Pressure: AMBIENT / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY / Manufacturer: Varian / Model: UNITY / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.85BRUNGERstructure solution
VNMR5.1VRIANprocessing
X-PLOR3.85BRUNGERrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE REFINED STRUCTURES ARE BASED ON A TOTAL OF 434 INTERPROTON DISTANCE RESTRAINTS, 27 3JHNHA COUPLING CONSTANT RESTRAINTS, AND 136 PROTON CHEMICAL SHIFT RESTRAINTS
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 18 / Conformers submitted total number: 18

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