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- PDB-1ohm: Sakacin P variant that is structurally stabilized by an inserted ... -

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Basic information

Entry
Database: PDB / ID: 1ohm
TitleSakacin P variant that is structurally stabilized by an inserted C-terminal disulfide bridge.
ComponentsBACTERIOCIN SAKACIN P
KeywordsANTIBIOTIC / PEDIOCIN-LIKE BACTERIOCINS / ANTIMICROBIAL PEPTIDES / SAKACIN ANTIBIOTIC / 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 sakacin-P
Function and homology information
Biological speciesLACTOBACILLUS SAKE (bacteria)
MethodSOLUTION NMR / MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsUteng, M. / Hauge, H.H. / Markwick, P.R. / Fimland, G. / Mantzilas, D. / Nissen-Meyer, J. / Muhle-Goll, C.
CitationJournal: Biochemistry / Year: 2003
Title: Three-Dimensional Structure in Lipid Micelles of the Pediocin-Like Antimicrobial Peptide Sakacin P and a Sakacin P Variant that is Structurally Stabilized by an Inserted C-Terminal Disulfide Bridge
Authors: Uteng, M. / Hauge, H.H. / Markwick, P.R. / Fimland, G. / Mantzilas, D. / Nissen-Meyer, J. / Muhle-Goll, C.
History
DepositionMay 28, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERIOCIN SAKACIN P


Theoretical massNumber of molelcules
Total (without water)4,5341
Polymers4,5341
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)10 / 50LEAST RESTRAIN VIOLATION AND OVERALL ENERGY
RepresentativeModel #1

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Components

#1: Protein/peptide BACTERIOCIN SAKACIN P / SAKACIN 674


Mass: 4534.000 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN INSERTED C-TERMINAL DISULFIDE BRIDGE.
Source: (gene. exp.) LACTOBACILLUS SAKE (bacteria) / Strain: LB790 / Variant: LB790/PGF10 / Plasmid: PGF10 / Production host: LACTOBACILLUS SAKE (bacteria) / Strain (production host): LB790 / Variant (production host): LB790/PGF10 / References: UniProt: P35618
Compound detailsENGINEERED MUTATION IN CHAIN A: CYS 42 TO ASN 42 SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED ...ENGINEERED MUTATION IN CHAIN A: CYS 42 TO ASN 42 SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN INSERTED C-TERMINAL DISULFIDE BRIDGE.
Has protein modificationY
Sequence detailsTHE SEQUENCE IS DESCRIBED IN J. BACTERIOL. 182, 2643-2648

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NOESY TOCSY
NMR detailsText: THE STRUCTURES WERE DETERMINED USING A COMBINATION OF 1H NMR SPECTROSCOPIC METHODS FOLLOWED BY DISTANCE GEOMETRY/SIMULATED ANNEALING CALCULATIONS.

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Sample preparation

DetailsContents: 250 MM DPC/10% D2O/ 0.1% TFA/1MM PEPTIDE
Sample conditionspH: 2.8 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Amber6CASE, D.A., PEARLMAN, D.A., CALDWELL, III, J.C., ET AL.refinement
ARIAstructure solution
Amberstructure solution
RefinementMethod: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: AMBER 6, SAN FRANCISCO, UNIVERSITY OF CALIFORNIA, 1999.
NMR ensembleConformer selection criteria: LEAST RESTRAIN VIOLATION AND OVERALL ENERGY
Conformers calculated total number: 50 / Conformers submitted total number: 10

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