- PDB-1og7: Three-dimensional structure in lipid micelles of the pediocin-lik... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1og7
Title
Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide sakacin P.
Components
BACTERIOCIN SAKACIN P
Keywords
ANTIBIOTIC / PEDIOCIN-LIKE BACTERIOCINS / ANTIMICROBIAL PEPTIDES / SAKACIN P
Function / homology
Function and homology information
killing of cells of another organism / defense response to bacterium / extracellular region Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #130 / Bacteriocin class IIa domain superfamily / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Class II bacteriocin / Bacteriocin class IIa family signature. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
BACTERICIDAL ACTIVITY; INHIBITS LISTERIA AND MANY LACTOBACILLI SPECIES.
Sequence details
THE SEQUENCE IS DESCRIBED IN J. BACTERIOL. 182, 2643-2648
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
NOESY
1
2
1
TOCSY
NMR details
Text: 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
Details
Contents: 90% TFE,0.1% TFA, 10% D2O,1MM PEPTIDE
Sample conditions
pH: 2.8 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR
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NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DRX
Bruker
DRX
500
1
Bruker DRX
Bruker
DRX
600
2
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Processing
NMR software
Name
Version
Developer
Classification
AMBER
6
CASE, D.A., PEARLMAN, D.A., CALDWELL, III, J.C., ETAL.
refinement
ARIA
structuresolution
AMBER
structuresolution
Refinement
Method: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1 Details: AMBER 6, SAN FRANCISCO, UNIVERSITY OF CALIFORNIA, 1999.
NMR ensemble
Conformer selection criteria: LEAST RESTRAIN VIOLATION AND OVERALL ENERGY Conformers calculated total number: 50 / Conformers submitted total number: 10
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